Structured Review

Abcam h3k9ac
Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in <t>H3K9ac</t> and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.
H3k9ac, supplied by Abcam, used in various techniques. Bioz Stars score: 92/100, based on 96 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/h3k9ac/product/Abcam
Average 92 stars, based on 96 article reviews
Price from $9.99 to $1999.99
h3k9ac - by Bioz Stars, 2020-05
92/100 stars

Images

1) Product Images from "Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers"

Article Title: Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkx1225

Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in H3K9ac and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.
Figure Legend Snippet: Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in H3K9ac and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.

Techniques Used: Staining, Flow Cytometry, Cytometry, Concentration Assay, Chromatin Immunoprecipitation

Dose dependent largazole effects on the epigenetic features of distal enhancer elements. ( A and B ) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) ( 23 ), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) ( 24 ). ( C ) and ( D ) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical ( n = 8667) and poised ( n = 3505) enhancers were used for further cluster analyses. ( E and F ) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).
Figure Legend Snippet: Dose dependent largazole effects on the epigenetic features of distal enhancer elements. ( A and B ) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) ( 23 ), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) ( 24 ). ( C ) and ( D ) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical ( n = 8667) and poised ( n = 3505) enhancers were used for further cluster analyses. ( E and F ) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).

Techniques Used: Chromatin Immunoprecipitation, Isolation, Activation Assay

Distinct H3K9 and H3K27 hyperacetylation responsive patterns upon largazole treatment. ( A ) A representative genomic snapshot of H3K27ac peaks illustrating different responses of gene bodies to newly acetylated histones. The signal initiates from the TSS (red dotted rectangle) of the FAT1 gene (orange panel) and spreads into the coding region or as in the case of CYP4V2 (purple panel), the preexisting acetylated TSS remains unmodified throughout all largazole dose treatments. Genes that do not show H3K9 or –K27 acetylation at the TSS (green panel) under basal conditions do not associate with the two histone marks as a result of largazole treatment. ( B ) Number of gene regions associated with the three response categories for H3K27ac (left) and H3K9ac (right). ( C ) Venn diagram showing the number of genes that exhibit new association with H3K27ac (green), H3K9ac (purple), and those that display both acetylation marks.
Figure Legend Snippet: Distinct H3K9 and H3K27 hyperacetylation responsive patterns upon largazole treatment. ( A ) A representative genomic snapshot of H3K27ac peaks illustrating different responses of gene bodies to newly acetylated histones. The signal initiates from the TSS (red dotted rectangle) of the FAT1 gene (orange panel) and spreads into the coding region or as in the case of CYP4V2 (purple panel), the preexisting acetylated TSS remains unmodified throughout all largazole dose treatments. Genes that do not show H3K9 or –K27 acetylation at the TSS (green panel) under basal conditions do not associate with the two histone marks as a result of largazole treatment. ( B ) Number of gene regions associated with the three response categories for H3K27ac (left) and H3K9ac (right). ( C ) Venn diagram showing the number of genes that exhibit new association with H3K27ac (green), H3K9ac (purple), and those that display both acetylation marks.

Techniques Used:

2) Product Images from "Analysis of Histones H3 and H4 Reveals Novel and Conserved Post-Translational Modifications in Sugarcane"

Article Title: Analysis of Histones H3 and H4 Reveals Novel and Conserved Post-Translational Modifications in Sugarcane

Journal: PLoS ONE

doi: 10.1371/journal.pone.0134586

Distribution patterns of histone post-translational modifications in sugarcane. (A) Immunoblot analysis of global histone H3 modifications in sugarcane tissues. (B) Sub-nuclear localization of H3K4me1, H3K4me3, H3K9me2, H3K27me3 and H3K9ac. (C) Chromatin distribution of sugarcane and Arabidopsis; white arrows show DAPI densely stained regions in sugarcane, representing heterochromatic blocks. In Arabidopsis, the chromocenters are well defined regions of heterochromatin (yellow arrows). (D) H3T3ph (red signals) does not co-localize with actively transcribed regions rich in RNA Polymerase II (green signals). Instead, it appears to be associated with silent chromatin; DAPI densely stained regions (grey nucleus, blue arrows) coincide with H3T3ph brighter foci (red nucleus, blue arrows), whereas weaker/absent H3T3ph regions (red nucleus, orange arrows) coincide with the less condensed chromatin poorly stained with DAPI (grey nucleus, orange arrows). Bars = 5 μm.
Figure Legend Snippet: Distribution patterns of histone post-translational modifications in sugarcane. (A) Immunoblot analysis of global histone H3 modifications in sugarcane tissues. (B) Sub-nuclear localization of H3K4me1, H3K4me3, H3K9me2, H3K27me3 and H3K9ac. (C) Chromatin distribution of sugarcane and Arabidopsis; white arrows show DAPI densely stained regions in sugarcane, representing heterochromatic blocks. In Arabidopsis, the chromocenters are well defined regions of heterochromatin (yellow arrows). (D) H3T3ph (red signals) does not co-localize with actively transcribed regions rich in RNA Polymerase II (green signals). Instead, it appears to be associated with silent chromatin; DAPI densely stained regions (grey nucleus, blue arrows) coincide with H3T3ph brighter foci (red nucleus, blue arrows), whereas weaker/absent H3T3ph regions (red nucleus, orange arrows) coincide with the less condensed chromatin poorly stained with DAPI (grey nucleus, orange arrows). Bars = 5 μm.

Techniques Used: Staining

3) Product Images from "GATA-1 Inhibits PU.1 Gene via DNA and Histone H3K9 Methylation of Its Distal Enhancer in Erythroleukemia"

Article Title: GATA-1 Inhibits PU.1 Gene via DNA and Histone H3K9 Methylation of Its Distal Enhancer in Erythroleukemia

Journal: PLoS ONE

doi: 10.1371/journal.pone.0152234

Repressive histone modifications following GATA-1 overexpression in AML-ELs. ChIP at the PU . 1 gene locus was carried out for the H3K9Me3, H3K27Me3, and H3K9Ac histone tail modifications in OCI-M2 (left) and K562 (right) cells. Grey bars: control cells, dark bars: 48hrs after GATA-1 transgene transfection. Data are relative to control antibody IPs (Y axis). T-test significance: p
Figure Legend Snippet: Repressive histone modifications following GATA-1 overexpression in AML-ELs. ChIP at the PU . 1 gene locus was carried out for the H3K9Me3, H3K27Me3, and H3K9Ac histone tail modifications in OCI-M2 (left) and K562 (right) cells. Grey bars: control cells, dark bars: 48hrs after GATA-1 transgene transfection. Data are relative to control antibody IPs (Y axis). T-test significance: p

Techniques Used: Over Expression, Chromatin Immunoprecipitation, Transfection

4) Product Images from "Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers"

Article Title: Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkx1225

Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in H3K9ac and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.
Figure Legend Snippet: Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in H3K9ac and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.

Techniques Used: Staining, Flow Cytometry, Cytometry, Concentration Assay, Chromatin Immunoprecipitation

Dose dependent largazole effects on the epigenetic features of distal enhancer elements. ( A and B ) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) ( 23 ), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) ( 24 ). ( C ) and ( D ) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical ( n = 8667) and poised ( n = 3505) enhancers were used for further cluster analyses. ( E and F ) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).
Figure Legend Snippet: Dose dependent largazole effects on the epigenetic features of distal enhancer elements. ( A and B ) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) ( 23 ), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) ( 24 ). ( C ) and ( D ) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical ( n = 8667) and poised ( n = 3505) enhancers were used for further cluster analyses. ( E and F ) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).

Techniques Used: Chromatin Immunoprecipitation, Isolation, Activation Assay

Distinct H3K9 and H3K27 hyperacetylation responsive patterns upon largazole treatment. ( A ) A representative genomic snapshot of H3K27ac peaks illustrating different responses of gene bodies to newly acetylated histones. The signal initiates from the TSS (red dotted rectangle) of the FAT1 gene (orange panel) and spreads into the coding region or as in the case of CYP4V2 (purple panel), the preexisting acetylated TSS remains unmodified throughout all largazole dose treatments. Genes that do not show H3K9 or –K27 acetylation at the TSS (green panel) under basal conditions do not associate with the two histone marks as a result of largazole treatment. ( B ) Number of gene regions associated with the three response categories for H3K27ac (left) and H3K9ac (right). ( C ) Venn diagram showing the number of genes that exhibit new association with H3K27ac (green), H3K9ac (purple), and those that display both acetylation marks.
Figure Legend Snippet: Distinct H3K9 and H3K27 hyperacetylation responsive patterns upon largazole treatment. ( A ) A representative genomic snapshot of H3K27ac peaks illustrating different responses of gene bodies to newly acetylated histones. The signal initiates from the TSS (red dotted rectangle) of the FAT1 gene (orange panel) and spreads into the coding region or as in the case of CYP4V2 (purple panel), the preexisting acetylated TSS remains unmodified throughout all largazole dose treatments. Genes that do not show H3K9 or –K27 acetylation at the TSS (green panel) under basal conditions do not associate with the two histone marks as a result of largazole treatment. ( B ) Number of gene regions associated with the three response categories for H3K27ac (left) and H3K9ac (right). ( C ) Venn diagram showing the number of genes that exhibit new association with H3K27ac (green), H3K9ac (purple), and those that display both acetylation marks.

Techniques Used:

5) Product Images from "The Carboxyl Terminus of Rtt109 Functions in Chaperone Control of Histone Acetylation"

Article Title: The Carboxyl Terminus of Rtt109 Functions in Chaperone Control of Histone Acetylation

Journal: Eukaryotic Cell

doi: 10.1128/EC.00291-12

The carboxyl terminus of fungal Rtt109s contain a Lys/Arg-rich sequence which is essential for H3K9ac in S. cerevisiae . (A) Using the ClustalW algorithm, S. cerevisiae Rtt109 was aligned with predicted Rtt109 sequences from fungi of the Ascomycota , Basidiomycota
Figure Legend Snippet: The carboxyl terminus of fungal Rtt109s contain a Lys/Arg-rich sequence which is essential for H3K9ac in S. cerevisiae . (A) Using the ClustalW algorithm, S. cerevisiae Rtt109 was aligned with predicted Rtt109 sequences from fungi of the Ascomycota , Basidiomycota

Techniques Used: Sequencing

Lysine 290 of Rtt109 is important for in vivo H3K56ac and H3K9ac. (A) 12MYC-RTT109K290Q rtt109 Δ and 12MYC-RTT109K290R rtt109 Δ strains show significantly decreased levels of H3K9ac but not H3K56ac in vivo . Western blotting was performed
Figure Legend Snippet: Lysine 290 of Rtt109 is important for in vivo H3K56ac and H3K9ac. (A) 12MYC-RTT109K290Q rtt109 Δ and 12MYC-RTT109K290R rtt109 Δ strains show significantly decreased levels of H3K9ac but not H3K56ac in vivo . Western blotting was performed

Techniques Used: In Vivo, Western Blot

6) Product Images from "Coordinate Changes in Histone Modifications, mRNA Levels, and Metabolite Profiles in Clonal INS-1 832/13 ?-Cells Accompany Functional Adaptations to Lipotoxicity *"

Article Title: Coordinate Changes in Histone Modifications, mRNA Levels, and Metabolite Profiles in Clonal INS-1 832/13 ?-Cells Accompany Functional Adaptations to Lipotoxicity *

Journal: The Journal of Biological Chemistry

doi: 10.1074/jbc.M112.422527

mRNA expression and ChIP of H3K9Ac, H3K79me2, H4K4me3, and H3K27me3 in clonal INS-1 832/13 β-cells subjected to lipotoxicity. A , gene expression of 10 selected genes based on differential expression due to lipotoxicity in the microarray and two
Figure Legend Snippet: mRNA expression and ChIP of H3K9Ac, H3K79me2, H4K4me3, and H3K27me3 in clonal INS-1 832/13 β-cells subjected to lipotoxicity. A , gene expression of 10 selected genes based on differential expression due to lipotoxicity in the microarray and two

Techniques Used: Expressing, Chromatin Immunoprecipitation, Microarray

7) Product Images from "Mediator subunit MED25 links the jasmonate receptor to transcriptionally active chromatin"

Article Title: Mediator subunit MED25 links the jasmonate receptor to transcriptionally active chromatin

Journal: Proceedings of the National Academy of Sciences of the United States of America

doi: 10.1073/pnas.1710885114

Enrichment of H3K9ac on the chromatin of JAZ8 and ERF1 . ( A ) Schematic diagrams of JAZ8 , ERF1 , and the PCR amplicons indicated as letters A–D used for ChIP-qPCR. ( B ) ChIP-qPCR shows the enrichment of H3K9ac on the chromatin of JAZ8 and ERF1 . The
Figure Legend Snippet: Enrichment of H3K9ac on the chromatin of JAZ8 and ERF1 . ( A ) Schematic diagrams of JAZ8 , ERF1 , and the PCR amplicons indicated as letters A–D used for ChIP-qPCR. ( B ) ChIP-qPCR shows the enrichment of H3K9ac on the chromatin of JAZ8 and ERF1 . The

Techniques Used: Polymerase Chain Reaction, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction

Depletion of HAC1 impairs JA-responsive gene expression and reduces H3K9ac accumulation on the promoters of JAZ8 and ERF1 . ( A ) qRT-PCR showing JA-Ile–induced expression of indicated genes in WT and hac1-4 . WT and hac1-4 plants were treated with
Figure Legend Snippet: Depletion of HAC1 impairs JA-responsive gene expression and reduces H3K9ac accumulation on the promoters of JAZ8 and ERF1 . ( A ) qRT-PCR showing JA-Ile–induced expression of indicated genes in WT and hac1-4 . WT and hac1-4 plants were treated with

Techniques Used: Expressing, Quantitative RT-PCR

8) Product Images from "The Carboxyl Terminus of Rtt109 Functions in Chaperone Control of Histone Acetylation"

Article Title: The Carboxyl Terminus of Rtt109 Functions in Chaperone Control of Histone Acetylation

Journal: Eukaryotic Cell

doi: 10.1128/EC.00291-12

The carboxyl terminus of fungal Rtt109s contain a Lys/Arg-rich sequence which is essential for H3K9ac in S. cerevisiae . (A) Using the ClustalW algorithm, S. cerevisiae Rtt109 was aligned with predicted Rtt109 sequences from fungi of the Ascomycota , Basidiomycota
Figure Legend Snippet: The carboxyl terminus of fungal Rtt109s contain a Lys/Arg-rich sequence which is essential for H3K9ac in S. cerevisiae . (A) Using the ClustalW algorithm, S. cerevisiae Rtt109 was aligned with predicted Rtt109 sequences from fungi of the Ascomycota , Basidiomycota

Techniques Used: Sequencing

Lysine 290 of Rtt109 is important for in vivo H3K56ac and H3K9ac. (A) 12MYC-RTT109K290Q rtt109 Δ and 12MYC-RTT109K290R rtt109 Δ strains show significantly decreased levels of H3K9ac but not H3K56ac in vivo . Western blotting was performed
Figure Legend Snippet: Lysine 290 of Rtt109 is important for in vivo H3K56ac and H3K9ac. (A) 12MYC-RTT109K290Q rtt109 Δ and 12MYC-RTT109K290R rtt109 Δ strains show significantly decreased levels of H3K9ac but not H3K56ac in vivo . Western blotting was performed

Techniques Used: In Vivo, Western Blot

9) Product Images from "Coordinate Changes in Histone Modifications, mRNA Levels, and Metabolite Profiles in Clonal INS-1 832/13 ?-Cells Accompany Functional Adaptations to Lipotoxicity *"

Article Title: Coordinate Changes in Histone Modifications, mRNA Levels, and Metabolite Profiles in Clonal INS-1 832/13 ?-Cells Accompany Functional Adaptations to Lipotoxicity *

Journal: The Journal of Biological Chemistry

doi: 10.1074/jbc.M112.422527

mRNA expression and ChIP of H3K9Ac, H3K79me2, H4K4me3, and H3K27me3 in clonal INS-1 832/13 β-cells subjected to lipotoxicity. A , gene expression of 10 selected genes based on differential expression due to lipotoxicity in the microarray and two
Figure Legend Snippet: mRNA expression and ChIP of H3K9Ac, H3K79me2, H4K4me3, and H3K27me3 in clonal INS-1 832/13 β-cells subjected to lipotoxicity. A , gene expression of 10 selected genes based on differential expression due to lipotoxicity in the microarray and two

Techniques Used: Expressing, Chromatin Immunoprecipitation, Microarray

10) Product Images from "Directed evolution of SIRT6 for improved deacylation and glucose homeostasis maintenance"

Article Title: Directed evolution of SIRT6 for improved deacylation and glucose homeostasis maintenance

Journal: Scientific Reports

doi: 10.1038/s41598-018-21887-9

SIRT6 deacetylation of H3K9Ac and H3K56ac in MEFs. SIRT6 deacetylation activity was measured using western blot analysis with specific antibodies. Analysis was performed on crude cell lysates prepared from equal amount of KO MEFs cells that stably express the different SIRT6 variants, including WT, D1, 6A4 and the non-catalytic H133Y (HY). ( A ) Western blot analysis, the line highlights the deletion of non-relevant mutant’s analysis from the gel (original blots are shown in Supplementary Fig. S9 ) ( B ) Quantification of the western blot by image J to assess the activities of the D1 and 6A4 mutants relative to the WT and HY mutant. The western blot analysis is a representative gel from three independent repeats.
Figure Legend Snippet: SIRT6 deacetylation of H3K9Ac and H3K56ac in MEFs. SIRT6 deacetylation activity was measured using western blot analysis with specific antibodies. Analysis was performed on crude cell lysates prepared from equal amount of KO MEFs cells that stably express the different SIRT6 variants, including WT, D1, 6A4 and the non-catalytic H133Y (HY). ( A ) Western blot analysis, the line highlights the deletion of non-relevant mutant’s analysis from the gel (original blots are shown in Supplementary Fig. S9 ) ( B ) Quantification of the western blot by image J to assess the activities of the D1 and 6A4 mutants relative to the WT and HY mutant. The western blot analysis is a representative gel from three independent repeats.

Techniques Used: Activity Assay, Western Blot, Stable Transfection, Mutagenesis

11) Product Images from "Loss of ABAT-Mediated GABAergic System Promotes Basal-Like Breast Cancer Progression by Activating Ca2+-NFAT1 Axis"

Article Title: Loss of ABAT-Mediated GABAergic System Promotes Basal-Like Breast Cancer Progression by Activating Ca2+-NFAT1 Axis

Journal: Theranostics

doi: 10.7150/thno.29407

Loss of ABAT results from Snail-mediated transcriptional repression. (A) Analysis of TCGA dataset for the expression of ABAT and Snail. The relative level of ABAT was plotted against that of Snail. (B) Box-plots indicate Snail mRNA expression in different subtypes of breast cancer from the TCGA dataset. (C) Analysis of GSE29672 and GSE58252 datasets for ABAT mRNA expression in MCF7 cells with or without Snail expression. (D-E) Expression of ABAT and Snail was analyzed by Western blotting (D) and quantitative real-time PCR (E) in BT483, HCC1428 and MCF7 cells infected with empty vector or Snail-expressing vector. (F) Schematic diagram showing positions of potential Snail-binding E-boxes in the ABAT promoter. ABAT promoter luciferase constructs and mutated derivative are also shown. (G) ABAT promoter luciferase construct (FL1) was co-expressed with empty vector or Snail-expressing vector in BT483, HCC1428 and MCF7 cells. After 48 h, luciferase activities were analyzed (mean ± SD in three separate experiments). (H) ABAT promoter luciferase constructs (FL1, FL2, FL3, and FL4) were co-expressed with empty vector or Snail-expressing vector in HEK-293T cells. Luciferase activities were analyzed as in (G). (I) ABAT promoter luciferase construct (FL1) as well as its mutant (mut) were co-expressed with empty vector or Snail-expressing vector in HEK-293T cells. Luciferase activities were analyzed as in (G). (J) The association of Snail and G9a, and the levels of H3K9me2 and H3K9Ac in the ABAT promoter in cells from (D) were analyzed by ChIP.
Figure Legend Snippet: Loss of ABAT results from Snail-mediated transcriptional repression. (A) Analysis of TCGA dataset for the expression of ABAT and Snail. The relative level of ABAT was plotted against that of Snail. (B) Box-plots indicate Snail mRNA expression in different subtypes of breast cancer from the TCGA dataset. (C) Analysis of GSE29672 and GSE58252 datasets for ABAT mRNA expression in MCF7 cells with or without Snail expression. (D-E) Expression of ABAT and Snail was analyzed by Western blotting (D) and quantitative real-time PCR (E) in BT483, HCC1428 and MCF7 cells infected with empty vector or Snail-expressing vector. (F) Schematic diagram showing positions of potential Snail-binding E-boxes in the ABAT promoter. ABAT promoter luciferase constructs and mutated derivative are also shown. (G) ABAT promoter luciferase construct (FL1) was co-expressed with empty vector or Snail-expressing vector in BT483, HCC1428 and MCF7 cells. After 48 h, luciferase activities were analyzed (mean ± SD in three separate experiments). (H) ABAT promoter luciferase constructs (FL1, FL2, FL3, and FL4) were co-expressed with empty vector or Snail-expressing vector in HEK-293T cells. Luciferase activities were analyzed as in (G). (I) ABAT promoter luciferase construct (FL1) as well as its mutant (mut) were co-expressed with empty vector or Snail-expressing vector in HEK-293T cells. Luciferase activities were analyzed as in (G). (J) The association of Snail and G9a, and the levels of H3K9me2 and H3K9Ac in the ABAT promoter in cells from (D) were analyzed by ChIP.

Techniques Used: Expressing, Western Blot, Real-time Polymerase Chain Reaction, Infection, Plasmid Preparation, Binding Assay, Luciferase, Construct, Mutagenesis, Chromatin Immunoprecipitation

12) Product Images from "Baf60b-mediated ATM-p53 activation blocks cell identity conversion by sensing chromatin opening"

Article Title: Baf60b-mediated ATM-p53 activation blocks cell identity conversion by sensing chromatin opening

Journal: Cell Research

doi: 10.1038/cr.2017.36

Baf60b links chromatin opening and ATM activation. (A) The binding of Baf60b at the regulatory regions of the Albumin and Hnf4 α genes was determined by the ChIP-qPCR assay. (B) Chromatin opening at the Albumin and Hnf4 α genes was measured by the micrococcal nuclease (MNase) assay in Baf60b-knockdown (sh1-Baf60b) TTFs and scramble controls after 3TF transduction. (C) H3K9ac on the Albumin and Hnf4 α genes was examined in Baf60b-knockdown (sh1-Baf60b) TTFs and scramble controls by the ChIP-qPCR assay. (D) The binding of p-ATM to the Albumin and Hnf4 α genes was analyzed by the ChIP-qPCR assay. sh1-Baf60b-mediated Baf60b silencing attenuated the p-ATM binding. Data represent two independent experiments. Error bars indicate SD. * P
Figure Legend Snippet: Baf60b links chromatin opening and ATM activation. (A) The binding of Baf60b at the regulatory regions of the Albumin and Hnf4 α genes was determined by the ChIP-qPCR assay. (B) Chromatin opening at the Albumin and Hnf4 α genes was measured by the micrococcal nuclease (MNase) assay in Baf60b-knockdown (sh1-Baf60b) TTFs and scramble controls after 3TF transduction. (C) H3K9ac on the Albumin and Hnf4 α genes was examined in Baf60b-knockdown (sh1-Baf60b) TTFs and scramble controls by the ChIP-qPCR assay. (D) The binding of p-ATM to the Albumin and Hnf4 α genes was analyzed by the ChIP-qPCR assay. sh1-Baf60b-mediated Baf60b silencing attenuated the p-ATM binding. Data represent two independent experiments. Error bars indicate SD. * P

Techniques Used: Activation Assay, Binding Assay, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction, Transduction

Early molecular events during hepatic conversion. (A) Expression level of 3TF was measured by qRT-PCR at different time points after transduction. (B) Binding of 3TF to regulatory regions of the Albumin and Hnf4 α genes was analyzed by the ChIP assay. Distal and proximal binding sites were determined in Supplementary information, Figure S6 . Data represent two independent experiments. (C) Chromatin opening at the Albumin and Hnf4 α genes was measured by the micrococcal nuclease (MNase) digestion assay at different time points after 3TF transduction. Data represent two independent experiments. (D , E) Activated histone marks of H3K9ac (D) and H3K4me2 (E) on the Albumin and Hnf4 α genes were examined by the ChIP-qPCR assay at different time points after 3TF transduction. (F) 3TF-induced hepatic gene expression was measured by qRT-PCR at different time points compared to TTFs. (G) p-ATM and p-p53 (Ser15) levels were analyzed by western blot analyses at different time points. (H) Binding of p-ATM to regulatory regions of the Albumin and Hnf4 α genes was analyzed by the ChIP-qPCR assay at 48 h after 3TF transduction. Data represent two independent experiments. Error bars indicate SD. * P
Figure Legend Snippet: Early molecular events during hepatic conversion. (A) Expression level of 3TF was measured by qRT-PCR at different time points after transduction. (B) Binding of 3TF to regulatory regions of the Albumin and Hnf4 α genes was analyzed by the ChIP assay. Distal and proximal binding sites were determined in Supplementary information, Figure S6 . Data represent two independent experiments. (C) Chromatin opening at the Albumin and Hnf4 α genes was measured by the micrococcal nuclease (MNase) digestion assay at different time points after 3TF transduction. Data represent two independent experiments. (D , E) Activated histone marks of H3K9ac (D) and H3K4me2 (E) on the Albumin and Hnf4 α genes were examined by the ChIP-qPCR assay at different time points after 3TF transduction. (F) 3TF-induced hepatic gene expression was measured by qRT-PCR at different time points compared to TTFs. (G) p-ATM and p-p53 (Ser15) levels were analyzed by western blot analyses at different time points. (H) Binding of p-ATM to regulatory regions of the Albumin and Hnf4 α genes was analyzed by the ChIP-qPCR assay at 48 h after 3TF transduction. Data represent two independent experiments. Error bars indicate SD. * P

Techniques Used: Expressing, Quantitative RT-PCR, Transduction, Binding Assay, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction, Western Blot

13) Product Images from "Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers"

Article Title: Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkx1225

Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in H3K9ac and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.
Figure Legend Snippet: Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in H3K9ac and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.

Techniques Used: Staining, Flow Cytometry, Cytometry, Concentration Assay, Chromatin Immunoprecipitation

Dose dependent largazole effects on the epigenetic features of distal enhancer elements. ( A and B ) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) ( 23 ), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) ( 24 ). ( C ) and ( D ) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical ( n = 8667) and poised ( n = 3505) enhancers were used for further cluster analyses. ( E and F ) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).
Figure Legend Snippet: Dose dependent largazole effects on the epigenetic features of distal enhancer elements. ( A and B ) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) ( 23 ), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) ( 24 ). ( C ) and ( D ) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical ( n = 8667) and poised ( n = 3505) enhancers were used for further cluster analyses. ( E and F ) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).

Techniques Used: Chromatin Immunoprecipitation, Isolation, Activation Assay

Distinct H3K9 and H3K27 hyperacetylation responsive patterns upon largazole treatment. ( A ) A representative genomic snapshot of H3K27ac peaks illustrating different responses of gene bodies to newly acetylated histones. The signal initiates from the TSS (red dotted rectangle) of the FAT1 gene (orange panel) and spreads into the coding region or as in the case of CYP4V2 (purple panel), the preexisting acetylated TSS remains unmodified throughout all largazole dose treatments. Genes that do not show H3K9 or –K27 acetylation at the TSS (green panel) under basal conditions do not associate with the two histone marks as a result of largazole treatment. ( B ) Number of gene regions associated with the three response categories for H3K27ac (left) and H3K9ac (right). ( C ) Venn diagram showing the number of genes that exhibit new association with H3K27ac (green), H3K9ac (purple), and those that display both acetylation marks.
Figure Legend Snippet: Distinct H3K9 and H3K27 hyperacetylation responsive patterns upon largazole treatment. ( A ) A representative genomic snapshot of H3K27ac peaks illustrating different responses of gene bodies to newly acetylated histones. The signal initiates from the TSS (red dotted rectangle) of the FAT1 gene (orange panel) and spreads into the coding region or as in the case of CYP4V2 (purple panel), the preexisting acetylated TSS remains unmodified throughout all largazole dose treatments. Genes that do not show H3K9 or –K27 acetylation at the TSS (green panel) under basal conditions do not associate with the two histone marks as a result of largazole treatment. ( B ) Number of gene regions associated with the three response categories for H3K27ac (left) and H3K9ac (right). ( C ) Venn diagram showing the number of genes that exhibit new association with H3K27ac (green), H3K9ac (purple), and those that display both acetylation marks.

Techniques Used:

14) Product Images from "Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers"

Article Title: Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkx1225

Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in H3K9ac and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.
Figure Legend Snippet: Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in H3K9ac and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.

Techniques Used: Staining, Flow Cytometry, Cytometry, Concentration Assay, Chromatin Immunoprecipitation

Dose dependent largazole effects on the epigenetic features of distal enhancer elements. ( A and B ) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) ( 23 ), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) ( 24 ). ( C ) and ( D ) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical ( n = 8667) and poised ( n = 3505) enhancers were used for further cluster analyses. ( E and F ) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).
Figure Legend Snippet: Dose dependent largazole effects on the epigenetic features of distal enhancer elements. ( A and B ) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) ( 23 ), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) ( 24 ). ( C ) and ( D ) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical ( n = 8667) and poised ( n = 3505) enhancers were used for further cluster analyses. ( E and F ) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).

Techniques Used: Chromatin Immunoprecipitation, Isolation, Activation Assay

Distinct H3K9 and H3K27 hyperacetylation responsive patterns upon largazole treatment. ( A ) A representative genomic snapshot of H3K27ac peaks illustrating different responses of gene bodies to newly acetylated histones. The signal initiates from the TSS (red dotted rectangle) of the FAT1 gene (orange panel) and spreads into the coding region or as in the case of CYP4V2 (purple panel), the preexisting acetylated TSS remains unmodified throughout all largazole dose treatments. Genes that do not show H3K9 or –K27 acetylation at the TSS (green panel) under basal conditions do not associate with the two histone marks as a result of largazole treatment. ( B ) Number of gene regions associated with the three response categories for H3K27ac (left) and H3K9ac (right). ( C ) Venn diagram showing the number of genes that exhibit new association with H3K27ac (green), H3K9ac (purple), and those that display both acetylation marks.
Figure Legend Snippet: Distinct H3K9 and H3K27 hyperacetylation responsive patterns upon largazole treatment. ( A ) A representative genomic snapshot of H3K27ac peaks illustrating different responses of gene bodies to newly acetylated histones. The signal initiates from the TSS (red dotted rectangle) of the FAT1 gene (orange panel) and spreads into the coding region or as in the case of CYP4V2 (purple panel), the preexisting acetylated TSS remains unmodified throughout all largazole dose treatments. Genes that do not show H3K9 or –K27 acetylation at the TSS (green panel) under basal conditions do not associate with the two histone marks as a result of largazole treatment. ( B ) Number of gene regions associated with the three response categories for H3K27ac (left) and H3K9ac (right). ( C ) Venn diagram showing the number of genes that exhibit new association with H3K27ac (green), H3K9ac (purple), and those that display both acetylation marks.

Techniques Used:

15) Product Images from "Analysis of Histones H3 and H4 Reveals Novel and Conserved Post-Translational Modifications in Sugarcane"

Article Title: Analysis of Histones H3 and H4 Reveals Novel and Conserved Post-Translational Modifications in Sugarcane

Journal: PLoS ONE

doi: 10.1371/journal.pone.0134586

Distribution patterns of histone post-translational modifications in sugarcane. (A) Immunoblot analysis of global histone H3 modifications in sugarcane tissues. (B) Sub-nuclear localization of H3K4me1, H3K4me3, H3K9me2, H3K27me3 and H3K9ac. (C) Chromatin distribution of sugarcane and Arabidopsis; white arrows show DAPI densely stained regions in sugarcane, representing heterochromatic blocks. In Arabidopsis, the chromocenters are well defined regions of heterochromatin (yellow arrows). (D) H3T3ph (red signals) does not co-localize with actively transcribed regions rich in RNA Polymerase II (green signals). Instead, it appears to be associated with silent chromatin; DAPI densely stained regions (grey nucleus, blue arrows) coincide with H3T3ph brighter foci (red nucleus, blue arrows), whereas weaker/absent H3T3ph regions (red nucleus, orange arrows) coincide with the less condensed chromatin poorly stained with DAPI (grey nucleus, orange arrows). Bars = 5 μm.
Figure Legend Snippet: Distribution patterns of histone post-translational modifications in sugarcane. (A) Immunoblot analysis of global histone H3 modifications in sugarcane tissues. (B) Sub-nuclear localization of H3K4me1, H3K4me3, H3K9me2, H3K27me3 and H3K9ac. (C) Chromatin distribution of sugarcane and Arabidopsis; white arrows show DAPI densely stained regions in sugarcane, representing heterochromatic blocks. In Arabidopsis, the chromocenters are well defined regions of heterochromatin (yellow arrows). (D) H3T3ph (red signals) does not co-localize with actively transcribed regions rich in RNA Polymerase II (green signals). Instead, it appears to be associated with silent chromatin; DAPI densely stained regions (grey nucleus, blue arrows) coincide with H3T3ph brighter foci (red nucleus, blue arrows), whereas weaker/absent H3T3ph regions (red nucleus, orange arrows) coincide with the less condensed chromatin poorly stained with DAPI (grey nucleus, orange arrows). Bars = 5 μm.

Techniques Used: Staining

16) Product Images from "Gene regulatory networks in neural cell fate acquisition from genome-wide chromatin association of Geminin and Zic1"

Article Title: Gene regulatory networks in neural cell fate acquisition from genome-wide chromatin association of Geminin and Zic1

Journal: Scientific Reports

doi: 10.1038/srep37412

Geminin over-expression during neural cell fate acquisition promotes the expression of Gmnn-associated genes with Gmnn-dependent histone acetylation. ( A ) Clustering of a subset of Gmnn-associated genes that also exhibit Gmnn-dependent H3K9ac, by comparison with their expression levels in ES cells, embryonic CNS, and adult cortex. ( B ) Locations of Gmnn association or Gmnn-dependent H3K9ac are shown for several genes in ( A ) (WashU Epigenome Browser). ( C,D ) ES cells were transfected and selected to overexpress a Gmnn cDNA construct, and ( C ) qRTPCR and ( D ) immunoblotting demonstrate increased Gmnn expression levels at the mRNA and protein level. ( E ) Levels of expression of four Gmnn-associated genes were defined on days 1–3 of neural fate acquisition, with versus without Gmnn over-expression (Gmnn OE). Gene expression levels on each day of NE fate acquisition are expressed relative to ES = 1.0 and p-values shown (student’s t-test) compare expression with versus without Gmnn OE on each day of the NE fate acquistion: ** =
Figure Legend Snippet: Geminin over-expression during neural cell fate acquisition promotes the expression of Gmnn-associated genes with Gmnn-dependent histone acetylation. ( A ) Clustering of a subset of Gmnn-associated genes that also exhibit Gmnn-dependent H3K9ac, by comparison with their expression levels in ES cells, embryonic CNS, and adult cortex. ( B ) Locations of Gmnn association or Gmnn-dependent H3K9ac are shown for several genes in ( A ) (WashU Epigenome Browser). ( C,D ) ES cells were transfected and selected to overexpress a Gmnn cDNA construct, and ( C ) qRTPCR and ( D ) immunoblotting demonstrate increased Gmnn expression levels at the mRNA and protein level. ( E ) Levels of expression of four Gmnn-associated genes were defined on days 1–3 of neural fate acquisition, with versus without Gmnn over-expression (Gmnn OE). Gene expression levels on each day of NE fate acquisition are expressed relative to ES = 1.0 and p-values shown (student’s t-test) compare expression with versus without Gmnn OE on each day of the NE fate acquistion: ** =

Techniques Used: Over Expression, Expressing, Transfection, Construct

17) Product Images from "Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers"

Article Title: Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkx1225

Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in H3K9ac and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.
Figure Legend Snippet: Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in H3K9ac and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.

Techniques Used: Staining, Flow Cytometry, Cytometry, Concentration Assay, Chromatin Immunoprecipitation

Dose dependent largazole effects on the epigenetic features of distal enhancer elements. ( A and B ) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) ( 23 ), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) ( 24 ). ( C ) and ( D ) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical ( n = 8667) and poised ( n = 3505) enhancers were used for further cluster analyses. ( E and F ) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).
Figure Legend Snippet: Dose dependent largazole effects on the epigenetic features of distal enhancer elements. ( A and B ) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) ( 23 ), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) ( 24 ). ( C ) and ( D ) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical ( n = 8667) and poised ( n = 3505) enhancers were used for further cluster analyses. ( E and F ) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).

Techniques Used: Chromatin Immunoprecipitation, Isolation, Activation Assay

Distinct H3K9 and H3K27 hyperacetylation responsive patterns upon largazole treatment. ( A ) A representative genomic snapshot of H3K27ac peaks illustrating different responses of gene bodies to newly acetylated histones. The signal initiates from the TSS (red dotted rectangle) of the FAT1 gene (orange panel) and spreads into the coding region or as in the case of CYP4V2 (purple panel), the preexisting acetylated TSS remains unmodified throughout all largazole dose treatments. Genes that do not show H3K9 or –K27 acetylation at the TSS (green panel) under basal conditions do not associate with the two histone marks as a result of largazole treatment. ( B ) Number of gene regions associated with the three response categories for H3K27ac (left) and H3K9ac (right). ( C ) Venn diagram showing the number of genes that exhibit new association with H3K27ac (green), H3K9ac (purple), and those that display both acetylation marks.
Figure Legend Snippet: Distinct H3K9 and H3K27 hyperacetylation responsive patterns upon largazole treatment. ( A ) A representative genomic snapshot of H3K27ac peaks illustrating different responses of gene bodies to newly acetylated histones. The signal initiates from the TSS (red dotted rectangle) of the FAT1 gene (orange panel) and spreads into the coding region or as in the case of CYP4V2 (purple panel), the preexisting acetylated TSS remains unmodified throughout all largazole dose treatments. Genes that do not show H3K9 or –K27 acetylation at the TSS (green panel) under basal conditions do not associate with the two histone marks as a result of largazole treatment. ( B ) Number of gene regions associated with the three response categories for H3K27ac (left) and H3K9ac (right). ( C ) Venn diagram showing the number of genes that exhibit new association with H3K27ac (green), H3K9ac (purple), and those that display both acetylation marks.

Techniques Used:

18) Product Images from "Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers"

Article Title: Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkx1225

Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in H3K9ac and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.
Figure Legend Snippet: Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in H3K9ac and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.

Techniques Used: Staining, Flow Cytometry, Cytometry, Concentration Assay, Chromatin Immunoprecipitation

Dose dependent largazole effects on the epigenetic features of distal enhancer elements. ( A and B ) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) ( 23 ), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) ( 24 ). ( C ) and ( D ) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical ( n = 8667) and poised ( n = 3505) enhancers were used for further cluster analyses. ( E and F ) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).
Figure Legend Snippet: Dose dependent largazole effects on the epigenetic features of distal enhancer elements. ( A and B ) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) ( 23 ), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) ( 24 ). ( C ) and ( D ) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical ( n = 8667) and poised ( n = 3505) enhancers were used for further cluster analyses. ( E and F ) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).

Techniques Used: Chromatin Immunoprecipitation, Isolation, Activation Assay

Distinct H3K9 and H3K27 hyperacetylation responsive patterns upon largazole treatment. ( A ) A representative genomic snapshot of H3K27ac peaks illustrating different responses of gene bodies to newly acetylated histones. The signal initiates from the TSS (red dotted rectangle) of the FAT1 gene (orange panel) and spreads into the coding region or as in the case of CYP4V2 (purple panel), the preexisting acetylated TSS remains unmodified throughout all largazole dose treatments. Genes that do not show H3K9 or –K27 acetylation at the TSS (green panel) under basal conditions do not associate with the two histone marks as a result of largazole treatment. ( B ) Number of gene regions associated with the three response categories for H3K27ac (left) and H3K9ac (right). ( C ) Venn diagram showing the number of genes that exhibit new association with H3K27ac (green), H3K9ac (purple), and those that display both acetylation marks.
Figure Legend Snippet: Distinct H3K9 and H3K27 hyperacetylation responsive patterns upon largazole treatment. ( A ) A representative genomic snapshot of H3K27ac peaks illustrating different responses of gene bodies to newly acetylated histones. The signal initiates from the TSS (red dotted rectangle) of the FAT1 gene (orange panel) and spreads into the coding region or as in the case of CYP4V2 (purple panel), the preexisting acetylated TSS remains unmodified throughout all largazole dose treatments. Genes that do not show H3K9 or –K27 acetylation at the TSS (green panel) under basal conditions do not associate with the two histone marks as a result of largazole treatment. ( B ) Number of gene regions associated with the three response categories for H3K27ac (left) and H3K9ac (right). ( C ) Venn diagram showing the number of genes that exhibit new association with H3K27ac (green), H3K9ac (purple), and those that display both acetylation marks.

Techniques Used:

19) Product Images from "The Carboxyl Terminus of Rtt109 Functions in Chaperone Control of Histone Acetylation"

Article Title: The Carboxyl Terminus of Rtt109 Functions in Chaperone Control of Histone Acetylation

Journal: Eukaryotic Cell

doi: 10.1128/EC.00291-12

The carboxyl terminus of fungal Rtt109s contain a Lys/Arg-rich sequence which is essential for H3K9ac in S. cerevisiae . (A) Using the ClustalW algorithm, S. cerevisiae Rtt109 was aligned with predicted Rtt109 sequences from fungi of the Ascomycota , Basidiomycota
Figure Legend Snippet: The carboxyl terminus of fungal Rtt109s contain a Lys/Arg-rich sequence which is essential for H3K9ac in S. cerevisiae . (A) Using the ClustalW algorithm, S. cerevisiae Rtt109 was aligned with predicted Rtt109 sequences from fungi of the Ascomycota , Basidiomycota

Techniques Used: Sequencing

Lysine 290 of Rtt109 is important for in vivo H3K56ac and H3K9ac. (A) 12MYC-RTT109K290Q rtt109 Δ and 12MYC-RTT109K290R rtt109 Δ strains show significantly decreased levels of H3K9ac but not H3K56ac in vivo . Western blotting was performed
Figure Legend Snippet: Lysine 290 of Rtt109 is important for in vivo H3K56ac and H3K9ac. (A) 12MYC-RTT109K290Q rtt109 Δ and 12MYC-RTT109K290R rtt109 Δ strains show significantly decreased levels of H3K9ac but not H3K56ac in vivo . Western blotting was performed

Techniques Used: In Vivo, Western Blot

20) Product Images from "Differential effects of garcinol and curcumin on histone and p53 modifications in tumour cells"

Article Title: Differential effects of garcinol and curcumin on histone and p53 modifications in tumour cells

Journal: BMC Cancer

doi: 10.1186/1471-2407-13-37

Reprogramming of global histone modifications by garcinol and curcumin. (A) Nuclear staining of MCF7 breast cancer cells with antibodies detecting pan acetyl H3 (top panels) or pan acetyl H4 (bottom panels). Control shows typical staining in the absence of inhibitors (vehicle only), and the effect of treatment with HAT inhibitors at the indicated concentrations are also shown. Scalebar: 10 μm. (B C) Immunostaining of MCF7 cells following treatment with the indicated concentrations of curcumin or garcinol for 24 hours. Vehicle control is also shown. Histone PTM-specific antibodies were used to reveal H3K18Ac, H4K16Ac and H3K9Ac levels in response to treatment. Scalebar: 10μm. (D) Western blots on whole cell extracts of MCF7 cells. Cell extracts were prepared following 24 hours culture in the presence of HAT inhibitors (or vehicle control) at the indicated concentrations. Specific antibodies were used to detect bulk levels of H3K18Ac, H4K16Ac and H3K9Ac. Densitometry measurements were performed using Image J software [ 21 ]. The level of each histone PTM in controls (vehicle only, normalised to a loading control) was set to 1. (E) Western blots showing bulk levels of H3K18Ac in whole cell extracts of U2OS and SaOS2 osteosarcoma cells following exposure to 10 μM or 20 μM curcumin or garcinol (as indicated in increasing scale). Actin loading controls are also shown, and the data were quantified by Image J as in ( D ).
Figure Legend Snippet: Reprogramming of global histone modifications by garcinol and curcumin. (A) Nuclear staining of MCF7 breast cancer cells with antibodies detecting pan acetyl H3 (top panels) or pan acetyl H4 (bottom panels). Control shows typical staining in the absence of inhibitors (vehicle only), and the effect of treatment with HAT inhibitors at the indicated concentrations are also shown. Scalebar: 10 μm. (B C) Immunostaining of MCF7 cells following treatment with the indicated concentrations of curcumin or garcinol for 24 hours. Vehicle control is also shown. Histone PTM-specific antibodies were used to reveal H3K18Ac, H4K16Ac and H3K9Ac levels in response to treatment. Scalebar: 10μm. (D) Western blots on whole cell extracts of MCF7 cells. Cell extracts were prepared following 24 hours culture in the presence of HAT inhibitors (or vehicle control) at the indicated concentrations. Specific antibodies were used to detect bulk levels of H3K18Ac, H4K16Ac and H3K9Ac. Densitometry measurements were performed using Image J software [ 21 ]. The level of each histone PTM in controls (vehicle only, normalised to a loading control) was set to 1. (E) Western blots showing bulk levels of H3K18Ac in whole cell extracts of U2OS and SaOS2 osteosarcoma cells following exposure to 10 μM or 20 μM curcumin or garcinol (as indicated in increasing scale). Actin loading controls are also shown, and the data were quantified by Image J as in ( D ).

Techniques Used: Staining, HAT Assay, Immunostaining, Western Blot, Software

21) Product Images from "Analysis of Histones H3 and H4 Reveals Novel and Conserved Post-Translational Modifications in Sugarcane"

Article Title: Analysis of Histones H3 and H4 Reveals Novel and Conserved Post-Translational Modifications in Sugarcane

Journal: PLoS ONE

doi: 10.1371/journal.pone.0134586

Distribution patterns of histone post-translational modifications in sugarcane. (A) Immunoblot analysis of global histone H3 modifications in sugarcane tissues. (B) Sub-nuclear localization of H3K4me1, H3K4me3, H3K9me2, H3K27me3 and H3K9ac. (C) Chromatin distribution of sugarcane and Arabidopsis; white arrows show DAPI densely stained regions in sugarcane, representing heterochromatic blocks. In Arabidopsis, the chromocenters are well defined regions of heterochromatin (yellow arrows). (D) H3T3ph (red signals) does not co-localize with actively transcribed regions rich in RNA Polymerase II (green signals). Instead, it appears to be associated with silent chromatin; DAPI densely stained regions (grey nucleus, blue arrows) coincide with H3T3ph brighter foci (red nucleus, blue arrows), whereas weaker/absent H3T3ph regions (red nucleus, orange arrows) coincide with the less condensed chromatin poorly stained with DAPI (grey nucleus, orange arrows). Bars = 5 μm.
Figure Legend Snippet: Distribution patterns of histone post-translational modifications in sugarcane. (A) Immunoblot analysis of global histone H3 modifications in sugarcane tissues. (B) Sub-nuclear localization of H3K4me1, H3K4me3, H3K9me2, H3K27me3 and H3K9ac. (C) Chromatin distribution of sugarcane and Arabidopsis; white arrows show DAPI densely stained regions in sugarcane, representing heterochromatic blocks. In Arabidopsis, the chromocenters are well defined regions of heterochromatin (yellow arrows). (D) H3T3ph (red signals) does not co-localize with actively transcribed regions rich in RNA Polymerase II (green signals). Instead, it appears to be associated with silent chromatin; DAPI densely stained regions (grey nucleus, blue arrows) coincide with H3T3ph brighter foci (red nucleus, blue arrows), whereas weaker/absent H3T3ph regions (red nucleus, orange arrows) coincide with the less condensed chromatin poorly stained with DAPI (grey nucleus, orange arrows). Bars = 5 μm.

Techniques Used: Staining

22) Product Images from "Histone deacetylase inhibitor SAHA mediates mast cell death and epigenetic silencing of constitutively active D816V KIT in systemic mastocytosis"

Article Title: Histone deacetylase inhibitor SAHA mediates mast cell death and epigenetic silencing of constitutively active D816V KIT in systemic mastocytosis

Journal: Oncotarget

doi: 10.18632/oncotarget.14181

SAHA effects on ROSA KIT WT and ROSA KIT D816V cells A . SAHA induced a dose- and time-dependent decrease in viability, mainly due to apoptotic cell death, in ROSA cells. The effects were seen earlier and at lower SAHA concentrations in ROSA KIT D816V , where a significant decrease in viability was seen already at 24 h with 1.25 μM SAHA, compared to ROSA KIT WT . B . There was a significant decrease in percentage KIT positive cells in both cell lines in response to SAHA, and also here ROSA KIT D816V were more profoundly affected by SAHA. C . A significant increase in H3K9ac was seen for both ROSA KIT WT and ROSA KIT D816V cells. KIT was significantly decreased in ROSA KIT WT cells, however note that in the DMSO control, KIT is increasing significantly at 6 and 24 h compared to baseline, thus the results are difficult to interpret. For ROSA KIT D816V , there is a tendency to decrease in KIT at 24 h for both SAHA doses. *=p
Figure Legend Snippet: SAHA effects on ROSA KIT WT and ROSA KIT D816V cells A . SAHA induced a dose- and time-dependent decrease in viability, mainly due to apoptotic cell death, in ROSA cells. The effects were seen earlier and at lower SAHA concentrations in ROSA KIT D816V , where a significant decrease in viability was seen already at 24 h with 1.25 μM SAHA, compared to ROSA KIT WT . B . There was a significant decrease in percentage KIT positive cells in both cell lines in response to SAHA, and also here ROSA KIT D816V were more profoundly affected by SAHA. C . A significant increase in H3K9ac was seen for both ROSA KIT WT and ROSA KIT D816V cells. KIT was significantly decreased in ROSA KIT WT cells, however note that in the DMSO control, KIT is increasing significantly at 6 and 24 h compared to baseline, thus the results are difficult to interpret. For ROSA KIT D816V , there is a tendency to decrease in KIT at 24 h for both SAHA doses. *=p

Techniques Used:

23) Product Images from "Directed evolution of SIRT6 for improved deacylation and glucose homeostasis maintenance"

Article Title: Directed evolution of SIRT6 for improved deacylation and glucose homeostasis maintenance

Journal: Scientific Reports

doi: 10.1038/s41598-018-21887-9

SIRT6 deacetylation of H3K9Ac and H3K56ac in MEFs. SIRT6 deacetylation activity was measured using western blot analysis with specific antibodies. Analysis was performed on crude cell lysates prepared from equal amount of KO MEFs cells that stably express the different SIRT6 variants, including WT, D1, 6A4 and the non-catalytic H133Y (HY). ( A ) ( B ) Quantification of the western blot by image J to assess the activities of the D1 and 6A4 mutants relative to the WT and HY mutant. The western blot analysis is a representative gel from three independent repeats.
Figure Legend Snippet: SIRT6 deacetylation of H3K9Ac and H3K56ac in MEFs. SIRT6 deacetylation activity was measured using western blot analysis with specific antibodies. Analysis was performed on crude cell lysates prepared from equal amount of KO MEFs cells that stably express the different SIRT6 variants, including WT, D1, 6A4 and the non-catalytic H133Y (HY). ( A ) ( B ) Quantification of the western blot by image J to assess the activities of the D1 and 6A4 mutants relative to the WT and HY mutant. The western blot analysis is a representative gel from three independent repeats.

Techniques Used: Activity Assay, Western Blot, Stable Transfection, Mutagenesis

24) Product Images from "Differential Acetylation of Histone H3 at the Regulatory Region of OsDREB1b Promoter Facilitates Chromatin Remodelling and Transcription Activation during Cold Stress"

Article Title: Differential Acetylation of Histone H3 at the Regulatory Region of OsDREB1b Promoter Facilitates Chromatin Remodelling and Transcription Activation during Cold Stress

Journal: PLoS ONE

doi: 10.1371/journal.pone.0100343

Alteration of histone H3 modifications during cold stress. Relative change in Histone H3 acetylation (H3K9ac, H3K14ac, and H3K27ac) during cold stress at (A) region Ia (−232 to −40) and region III (+157 to +307) (B) region Ib (−415 to −246) and region II (−610 to −440) of OsDREB1b gene. (C) Relative change in histone modifications at promoter and upstream region of OsDREB2a during cold stress. Samples were analysed by real time PCR except (A). The mean values for each region were normalised to Actin promoter values. Error bar represent standard error (SE) where number of independent experiments (n) = 3. The significance of the results were analysed by student’s t test and the significant changes (P≤0.05) were marked by *. (C) Western blot showing H3K9ac, H3K14ac and H3K27ac signal in whole cell extract isolated from control and cold stress treated rice seedlings.
Figure Legend Snippet: Alteration of histone H3 modifications during cold stress. Relative change in Histone H3 acetylation (H3K9ac, H3K14ac, and H3K27ac) during cold stress at (A) region Ia (−232 to −40) and region III (+157 to +307) (B) region Ib (−415 to −246) and region II (−610 to −440) of OsDREB1b gene. (C) Relative change in histone modifications at promoter and upstream region of OsDREB2a during cold stress. Samples were analysed by real time PCR except (A). The mean values for each region were normalised to Actin promoter values. Error bar represent standard error (SE) where number of independent experiments (n) = 3. The significance of the results were analysed by student’s t test and the significant changes (P≤0.05) were marked by *. (C) Western blot showing H3K9ac, H3K14ac and H3K27ac signal in whole cell extract isolated from control and cold stress treated rice seedlings.

Techniques Used: IA, Real-time Polymerase Chain Reaction, Western Blot, Isolation

25) Product Images from "Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers"

Article Title: Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkx1225

Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in H3K9ac and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.
Figure Legend Snippet: Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in H3K9ac and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.

Techniques Used: Staining, Flow Cytometry, Cytometry, Concentration Assay, Chromatin Immunoprecipitation

Dose dependent largazole effects on the epigenetic features of distal enhancer elements. ( A and B ) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) ( 23 ), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) ( 24 ). ( C ) and ( D ) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical ( n = 8667) and poised ( n = 3505) enhancers were used for further cluster analyses. ( E and F ) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).
Figure Legend Snippet: Dose dependent largazole effects on the epigenetic features of distal enhancer elements. ( A and B ) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) ( 23 ), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) ( 24 ). ( C ) and ( D ) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical ( n = 8667) and poised ( n = 3505) enhancers were used for further cluster analyses. ( E and F ) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).

Techniques Used: Chromatin Immunoprecipitation, Isolation, Activation Assay

Distinct H3K9 and H3K27 hyperacetylation responsive patterns upon largazole treatment. ( A ) A representative genomic snapshot of H3K27ac peaks illustrating different responses of gene bodies to newly acetylated histones. The signal initiates from the TSS (red dotted rectangle) of the FAT1 gene (orange panel) and spreads into the coding region or as in the case of CYP4V2 (purple panel), the preexisting acetylated TSS remains unmodified throughout all largazole dose treatments. Genes that do not show H3K9 or –K27 acetylation at the TSS (green panel) under basal conditions do not associate with the two histone marks as a result of largazole treatment. ( B ) Number of gene regions associated with the three response categories for H3K27ac (left) and H3K9ac (right). ( C ) Venn diagram showing the number of genes that exhibit new association with H3K27ac (green), H3K9ac (purple), and those that display both acetylation marks.
Figure Legend Snippet: Distinct H3K9 and H3K27 hyperacetylation responsive patterns upon largazole treatment. ( A ) A representative genomic snapshot of H3K27ac peaks illustrating different responses of gene bodies to newly acetylated histones. The signal initiates from the TSS (red dotted rectangle) of the FAT1 gene (orange panel) and spreads into the coding region or as in the case of CYP4V2 (purple panel), the preexisting acetylated TSS remains unmodified throughout all largazole dose treatments. Genes that do not show H3K9 or –K27 acetylation at the TSS (green panel) under basal conditions do not associate with the two histone marks as a result of largazole treatment. ( B ) Number of gene regions associated with the three response categories for H3K27ac (left) and H3K9ac (right). ( C ) Venn diagram showing the number of genes that exhibit new association with H3K27ac (green), H3K9ac (purple), and those that display both acetylation marks.

Techniques Used:

26) Product Images from "Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers"

Article Title: Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkx1225

Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in H3K9ac and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.
Figure Legend Snippet: Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in H3K9ac and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.

Techniques Used: Staining, Flow Cytometry, Cytometry, Concentration Assay, Chromatin Immunoprecipitation

Dose dependent largazole effects on the epigenetic features of distal enhancer elements. ( A and B ) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) ( 23 ), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) ( 24 ). ( C ) and ( D ) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical ( n = 8667) and poised ( n = 3505) enhancers were used for further cluster analyses. ( E and F ) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).
Figure Legend Snippet: Dose dependent largazole effects on the epigenetic features of distal enhancer elements. ( A and B ) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) ( 23 ), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) ( 24 ). ( C ) and ( D ) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical ( n = 8667) and poised ( n = 3505) enhancers were used for further cluster analyses. ( E and F ) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).

Techniques Used: Chromatin Immunoprecipitation, Isolation, Activation Assay

Distinct H3K9 and H3K27 hyperacetylation responsive patterns upon largazole treatment. ( A ) A representative genomic snapshot of H3K27ac peaks illustrating different responses of gene bodies to newly acetylated histones. The signal initiates from the TSS (red dotted rectangle) of the FAT1 gene (orange panel) and spreads into the coding region or as in the case of CYP4V2 (purple panel), the preexisting acetylated TSS remains unmodified throughout all largazole dose treatments. Genes that do not show H3K9 or –K27 acetylation at the TSS (green panel) under basal conditions do not associate with the two histone marks as a result of largazole treatment. ( B ) Number of gene regions associated with the three response categories for H3K27ac (left) and H3K9ac (right). ( C ) Venn diagram showing the number of genes that exhibit new association with H3K27ac (green), H3K9ac (purple), and those that display both acetylation marks.
Figure Legend Snippet: Distinct H3K9 and H3K27 hyperacetylation responsive patterns upon largazole treatment. ( A ) A representative genomic snapshot of H3K27ac peaks illustrating different responses of gene bodies to newly acetylated histones. The signal initiates from the TSS (red dotted rectangle) of the FAT1 gene (orange panel) and spreads into the coding region or as in the case of CYP4V2 (purple panel), the preexisting acetylated TSS remains unmodified throughout all largazole dose treatments. Genes that do not show H3K9 or –K27 acetylation at the TSS (green panel) under basal conditions do not associate with the two histone marks as a result of largazole treatment. ( B ) Number of gene regions associated with the three response categories for H3K27ac (left) and H3K9ac (right). ( C ) Venn diagram showing the number of genes that exhibit new association with H3K27ac (green), H3K9ac (purple), and those that display both acetylation marks.

Techniques Used:

27) Product Images from "Dynamic Regulation of the Adenosine Kinase Gene during Early Postnatal Brain Development and Maturation"

Article Title: Dynamic Regulation of the Adenosine Kinase Gene during Early Postnatal Brain Development and Maturation

Journal: Frontiers in Molecular Neuroscience

doi: 10.3389/fnmol.2016.00099

Impact of epigenetic chromatin modifications on Adk-L promoter activity in P4 and P14 rat hippocampal neurons. (A) Promoter region of the long Adk isoform was analyzed from pos. −735 to + 470 relative to the TSS. (B) Activating histone modifications were identified at the Adk-L promoter in both P4 and P14 hippocampal neurons, including acetylation of H3 and H4, as well as H3 phosphoacetylation and lysine 4 trimethylation, with a relative sparing of the TSS. There was no evidence for repressive H3K27 trimethylation. Upper right corner of each diagram with insets showing enrichment of positive controls for each antibody presented as percent of the total input chromatin (% input). Adk-L promoter, promoter regulating long Adk isoform expression; ChIP, chromatin immunoprecipitation; H3K9ac, acetylation of lysine (K) 9 of histone H3; H4ac, pan-acetylation of histone H4; H3S10phK14ac, phosphoacetylation of histone H3 targeting Serine (S) 10 and Lysine (K) 14; H3K4me3, trimethylation of lysine (K) 4 of histone H3; H3K27me3, trimethylation of lysine (K) 27 of histone H3; TSS, transcriptional start site.
Figure Legend Snippet: Impact of epigenetic chromatin modifications on Adk-L promoter activity in P4 and P14 rat hippocampal neurons. (A) Promoter region of the long Adk isoform was analyzed from pos. −735 to + 470 relative to the TSS. (B) Activating histone modifications were identified at the Adk-L promoter in both P4 and P14 hippocampal neurons, including acetylation of H3 and H4, as well as H3 phosphoacetylation and lysine 4 trimethylation, with a relative sparing of the TSS. There was no evidence for repressive H3K27 trimethylation. Upper right corner of each diagram with insets showing enrichment of positive controls for each antibody presented as percent of the total input chromatin (% input). Adk-L promoter, promoter regulating long Adk isoform expression; ChIP, chromatin immunoprecipitation; H3K9ac, acetylation of lysine (K) 9 of histone H3; H4ac, pan-acetylation of histone H4; H3S10phK14ac, phosphoacetylation of histone H3 targeting Serine (S) 10 and Lysine (K) 14; H3K4me3, trimethylation of lysine (K) 4 of histone H3; H3K27me3, trimethylation of lysine (K) 27 of histone H3; TSS, transcriptional start site.

Techniques Used: Activity Assay, Expressing, Chromatin Immunoprecipitation

Impact of epigenetic chromatin modifications on Adk-S promoter activity in P4 and P14 rat hippocampal neurons. (A) Promoter region of the short Adk isoform was analyzed from pos. −1043 to +1084 relative to the TSS. (B) Enrichment of activating histone modifications at the Adk-S promoter in both P4 and P14 hippocampal neurons, including acetylation of H3 and H4, as well as H3 phosphoacetylation and lysine 4 trimethylation, particularly upstream of the TSS was identified. No evidence for repressive H3K27 trimethylation. Adk-S promoter, promoter regulating short Adk isoform expression; ChIP, chromatin immunoprecipitation; H3K9ac, acetylation of lysine (K) 9 of histone H3; H4ac, pan-acetylation of histone H4; H3S10phK14ac, phosphoacetylation of histone H3 targeting Serine (S) 10 and Lysine (K) 14; H3K4me3, trimethylation of lysine (K) 4 of histone H3; H3K27me3, trimethylation of lysine (K) 27 of histone H3; Hist1H4B, Histone cluster 1, H4B; MyoD, Myogenic differentiation 1; TSS, transcriptional start site.
Figure Legend Snippet: Impact of epigenetic chromatin modifications on Adk-S promoter activity in P4 and P14 rat hippocampal neurons. (A) Promoter region of the short Adk isoform was analyzed from pos. −1043 to +1084 relative to the TSS. (B) Enrichment of activating histone modifications at the Adk-S promoter in both P4 and P14 hippocampal neurons, including acetylation of H3 and H4, as well as H3 phosphoacetylation and lysine 4 trimethylation, particularly upstream of the TSS was identified. No evidence for repressive H3K27 trimethylation. Adk-S promoter, promoter regulating short Adk isoform expression; ChIP, chromatin immunoprecipitation; H3K9ac, acetylation of lysine (K) 9 of histone H3; H4ac, pan-acetylation of histone H4; H3S10phK14ac, phosphoacetylation of histone H3 targeting Serine (S) 10 and Lysine (K) 14; H3K4me3, trimethylation of lysine (K) 4 of histone H3; H3K27me3, trimethylation of lysine (K) 27 of histone H3; Hist1H4B, Histone cluster 1, H4B; MyoD, Myogenic differentiation 1; TSS, transcriptional start site.

Techniques Used: Activity Assay, Expressing, Chromatin Immunoprecipitation

28) Product Images from "Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers"

Article Title: Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkx1225

Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in H3K9ac and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.
Figure Legend Snippet: Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in H3K9ac and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.

Techniques Used: Staining, Flow Cytometry, Cytometry, Concentration Assay, Chromatin Immunoprecipitation

Dose dependent largazole effects on the epigenetic features of distal enhancer elements. ( A and B ) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) ( 23 ), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) ( 24 ). ( C ) and ( D ) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical ( n = 8667) and poised ( n = 3505) enhancers were used for further cluster analyses. ( E and F ) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).
Figure Legend Snippet: Dose dependent largazole effects on the epigenetic features of distal enhancer elements. ( A and B ) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) ( 23 ), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) ( 24 ). ( C ) and ( D ) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical ( n = 8667) and poised ( n = 3505) enhancers were used for further cluster analyses. ( E and F ) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).

Techniques Used: Chromatin Immunoprecipitation, Isolation, Activation Assay

Distinct H3K9 and H3K27 hyperacetylation responsive patterns upon largazole treatment. ( A ) A representative genomic snapshot of H3K27ac peaks illustrating different responses of gene bodies to newly acetylated histones. The signal initiates from the TSS (red dotted rectangle) of the FAT1 gene (orange panel) and spreads into the coding region or as in the case of CYP4V2 (purple panel), the preexisting acetylated TSS remains unmodified throughout all largazole dose treatments. Genes that do not show H3K9 or –K27 acetylation at the TSS (green panel) under basal conditions do not associate with the two histone marks as a result of largazole treatment. ( B ) Number of gene regions associated with the three response categories for H3K27ac (left) and H3K9ac (right). ( C ) Venn diagram showing the number of genes that exhibit new association with H3K27ac (green), H3K9ac (purple), and those that display both acetylation marks.
Figure Legend Snippet: Distinct H3K9 and H3K27 hyperacetylation responsive patterns upon largazole treatment. ( A ) A representative genomic snapshot of H3K27ac peaks illustrating different responses of gene bodies to newly acetylated histones. The signal initiates from the TSS (red dotted rectangle) of the FAT1 gene (orange panel) and spreads into the coding region or as in the case of CYP4V2 (purple panel), the preexisting acetylated TSS remains unmodified throughout all largazole dose treatments. Genes that do not show H3K9 or –K27 acetylation at the TSS (green panel) under basal conditions do not associate with the two histone marks as a result of largazole treatment. ( B ) Number of gene regions associated with the three response categories for H3K27ac (left) and H3K9ac (right). ( C ) Venn diagram showing the number of genes that exhibit new association with H3K27ac (green), H3K9ac (purple), and those that display both acetylation marks.

Techniques Used:

29) Product Images from "Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers"

Article Title: Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkx1225

Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in H3K9ac and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.
Figure Legend Snippet: Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in H3K9ac and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.

Techniques Used: Staining, Flow Cytometry, Cytometry, Concentration Assay, Chromatin Immunoprecipitation

Dose dependent largazole effects on the epigenetic features of distal enhancer elements. ( A and B ) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) ( 23 ), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) ( 24 ). ( C ) and ( D ) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical ( n = 8667) and poised ( n = 3505) enhancers were used for further cluster analyses. ( E and F ) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).
Figure Legend Snippet: Dose dependent largazole effects on the epigenetic features of distal enhancer elements. ( A and B ) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) ( 23 ), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) ( 24 ). ( C ) and ( D ) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical ( n = 8667) and poised ( n = 3505) enhancers were used for further cluster analyses. ( E and F ) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).

Techniques Used: Chromatin Immunoprecipitation, Isolation, Activation Assay

Distinct H3K9 and H3K27 hyperacetylation responsive patterns upon largazole treatment. ( A ) A representative genomic snapshot of H3K27ac peaks illustrating different responses of gene bodies to newly acetylated histones. The signal initiates from the TSS (red dotted rectangle) of the FAT1 gene (orange panel) and spreads into the coding region or as in the case of CYP4V2 (purple panel), the preexisting acetylated TSS remains unmodified throughout all largazole dose treatments. Genes that do not show H3K9 or –K27 acetylation at the TSS (green panel) under basal conditions do not associate with the two histone marks as a result of largazole treatment. ( B ) Number of gene regions associated with the three response categories for H3K27ac (left) and H3K9ac (right). ( C ) Venn diagram showing the number of genes that exhibit new association with H3K27ac (green), H3K9ac (purple), and those that display both acetylation marks.
Figure Legend Snippet: Distinct H3K9 and H3K27 hyperacetylation responsive patterns upon largazole treatment. ( A ) A representative genomic snapshot of H3K27ac peaks illustrating different responses of gene bodies to newly acetylated histones. The signal initiates from the TSS (red dotted rectangle) of the FAT1 gene (orange panel) and spreads into the coding region or as in the case of CYP4V2 (purple panel), the preexisting acetylated TSS remains unmodified throughout all largazole dose treatments. Genes that do not show H3K9 or –K27 acetylation at the TSS (green panel) under basal conditions do not associate with the two histone marks as a result of largazole treatment. ( B ) Number of gene regions associated with the three response categories for H3K27ac (left) and H3K9ac (right). ( C ) Venn diagram showing the number of genes that exhibit new association with H3K27ac (green), H3K9ac (purple), and those that display both acetylation marks.

Techniques Used:

30) Product Images from "The Carboxyl Terminus of Rtt109 Functions in Chaperone Control of Histone Acetylation"

Article Title: The Carboxyl Terminus of Rtt109 Functions in Chaperone Control of Histone Acetylation

Journal: Eukaryotic Cell

doi: 10.1128/EC.00291-12

The carboxyl terminus of fungal Rtt109s contain a Lys/Arg-rich sequence which is essential for H3K9ac in S. cerevisiae . (A) Using the ClustalW algorithm, S. cerevisiae Rtt109 was aligned with predicted Rtt109 sequences from fungi of the Ascomycota , Basidiomycota
Figure Legend Snippet: The carboxyl terminus of fungal Rtt109s contain a Lys/Arg-rich sequence which is essential for H3K9ac in S. cerevisiae . (A) Using the ClustalW algorithm, S. cerevisiae Rtt109 was aligned with predicted Rtt109 sequences from fungi of the Ascomycota , Basidiomycota

Techniques Used: Sequencing

Lysine 290 of Rtt109 is important for in vivo H3K56ac and H3K9ac. (A) 12MYC-RTT109K290Q rtt109 Δ and 12MYC-RTT109K290R rtt109 Δ strains show significantly decreased levels of H3K9ac but not H3K56ac in vivo . Western blotting was performed
Figure Legend Snippet: Lysine 290 of Rtt109 is important for in vivo H3K56ac and H3K9ac. (A) 12MYC-RTT109K290Q rtt109 Δ and 12MYC-RTT109K290R rtt109 Δ strains show significantly decreased levels of H3K9ac but not H3K56ac in vivo . Western blotting was performed

Techniques Used: In Vivo, Western Blot

31) Product Images from "Coordinate Changes in Histone Modifications, mRNA Levels, and Metabolite Profiles in Clonal INS-1 832/13 ?-Cells Accompany Functional Adaptations to Lipotoxicity *"

Article Title: Coordinate Changes in Histone Modifications, mRNA Levels, and Metabolite Profiles in Clonal INS-1 832/13 ?-Cells Accompany Functional Adaptations to Lipotoxicity *

Journal: The Journal of Biological Chemistry

doi: 10.1074/jbc.M112.422527

mRNA expression and ChIP of H3K9Ac, H3K79me2, H4K4me3, and H3K27me3 in clonal INS-1 832/13 β-cells subjected to lipotoxicity. A , gene expression of 10 selected genes based on differential expression due to lipotoxicity in the microarray and two
Figure Legend Snippet: mRNA expression and ChIP of H3K9Ac, H3K79me2, H4K4me3, and H3K27me3 in clonal INS-1 832/13 β-cells subjected to lipotoxicity. A , gene expression of 10 selected genes based on differential expression due to lipotoxicity in the microarray and two

Techniques Used: Expressing, Chromatin Immunoprecipitation, Microarray

32) Product Images from "Cxxc Finger Protein 1 Positively Regulates GM-CSF-Derived Macrophage Phagocytosis Through Csf2rα-Mediated Signaling"

Article Title: Cxxc Finger Protein 1 Positively Regulates GM-CSF-Derived Macrophage Phagocytosis Through Csf2rα-Mediated Signaling

Journal: Frontiers in Immunology

doi: 10.3389/fimmu.2018.01885

Cxxc finger protein 1 (CFP1) bound to the Csf2rα promoter region and was associated with H3K4me3, H3K9ac, and H3K27ac. (A,B) The expression of Csf2rα at the mRNA (A) and protein (B) level in wild-type (black rectangle) and CFP1-deficient (white rectangle) macrophages. (C) Immunoblot analysis of phosphorylated (p-) STAT5 and total STAT5 and GAPDH in wild-type and CFP1-deficient macrophages stimulated for 0–30 min (upper lanes) with GM-CSF (10 ng ml −1 ). (D) The expression of PU.1 at the mRNA level in wild-type (black rectangle) and CFP1-deficient (white rectangle) macrophages. (E–H) Chromatin immunoprecipitation analysis of endogenous CFP1 (E) , H3K4me3 (F) , H3K9ac (G) , H3K9ac (H) in wild-type (black rectangle) and CFP1-deficient (white rectangle) macrophages, followed by real-time PCR analysis for specific enrichment of each modification at the Csf2rα promoter. The primer positions are relative to the TSS of Csf2rα. The mean and SD of four independent experiments are shown. * P
Figure Legend Snippet: Cxxc finger protein 1 (CFP1) bound to the Csf2rα promoter region and was associated with H3K4me3, H3K9ac, and H3K27ac. (A,B) The expression of Csf2rα at the mRNA (A) and protein (B) level in wild-type (black rectangle) and CFP1-deficient (white rectangle) macrophages. (C) Immunoblot analysis of phosphorylated (p-) STAT5 and total STAT5 and GAPDH in wild-type and CFP1-deficient macrophages stimulated for 0–30 min (upper lanes) with GM-CSF (10 ng ml −1 ). (D) The expression of PU.1 at the mRNA level in wild-type (black rectangle) and CFP1-deficient (white rectangle) macrophages. (E–H) Chromatin immunoprecipitation analysis of endogenous CFP1 (E) , H3K4me3 (F) , H3K9ac (G) , H3K9ac (H) in wild-type (black rectangle) and CFP1-deficient (white rectangle) macrophages, followed by real-time PCR analysis for specific enrichment of each modification at the Csf2rα promoter. The primer positions are relative to the TSS of Csf2rα. The mean and SD of four independent experiments are shown. * P

Techniques Used: Expressing, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction, Modification

33) Product Images from "Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers"

Article Title: Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkx1225

Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in H3K9ac and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.
Figure Legend Snippet: Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in H3K9ac and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.

Techniques Used: Staining, Flow Cytometry, Cytometry, Concentration Assay, Chromatin Immunoprecipitation

Dose dependent largazole effects on the epigenetic features of distal enhancer elements. ( A and B ) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) ( 23 ), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) ( 24 ). ( C ) and ( D ) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical ( n = 8667) and poised ( n = 3505) enhancers were used for further cluster analyses. ( E and F ) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).
Figure Legend Snippet: Dose dependent largazole effects on the epigenetic features of distal enhancer elements. ( A and B ) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) ( 23 ), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) ( 24 ). ( C ) and ( D ) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical ( n = 8667) and poised ( n = 3505) enhancers were used for further cluster analyses. ( E and F ) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).

Techniques Used: Chromatin Immunoprecipitation, Isolation, Activation Assay

Distinct H3K9 and H3K27 hyperacetylation responsive patterns upon largazole treatment. ( A ) A representative genomic snapshot of H3K27ac peaks illustrating different responses of gene bodies to newly acetylated histones. The signal initiates from the TSS (red dotted rectangle) of the FAT1 gene (orange panel) and spreads into the coding region or as in the case of CYP4V2 (purple panel), the preexisting acetylated TSS remains unmodified throughout all largazole dose treatments. Genes that do not show H3K9 or –K27 acetylation at the TSS (green panel) under basal conditions do not associate with the two histone marks as a result of largazole treatment. ( B ) Number of gene regions associated with the three response categories for H3K27ac (left) and H3K9ac (right). ( C ) Venn diagram showing the number of genes that exhibit new association with H3K27ac (green), H3K9ac (purple), and those that display both acetylation marks.
Figure Legend Snippet: Distinct H3K9 and H3K27 hyperacetylation responsive patterns upon largazole treatment. ( A ) A representative genomic snapshot of H3K27ac peaks illustrating different responses of gene bodies to newly acetylated histones. The signal initiates from the TSS (red dotted rectangle) of the FAT1 gene (orange panel) and spreads into the coding region or as in the case of CYP4V2 (purple panel), the preexisting acetylated TSS remains unmodified throughout all largazole dose treatments. Genes that do not show H3K9 or –K27 acetylation at the TSS (green panel) under basal conditions do not associate with the two histone marks as a result of largazole treatment. ( B ) Number of gene regions associated with the three response categories for H3K27ac (left) and H3K9ac (right). ( C ) Venn diagram showing the number of genes that exhibit new association with H3K27ac (green), H3K9ac (purple), and those that display both acetylation marks.

Techniques Used:

34) Product Images from "Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers"

Article Title: Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkx1225

Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in H3K9ac and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.
Figure Legend Snippet: Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in H3K9ac and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.

Techniques Used: Staining, Flow Cytometry, Cytometry, Concentration Assay, Chromatin Immunoprecipitation

Dose dependent largazole effects on the epigenetic features of distal enhancer elements. ( A and B ) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) ( 23 ), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) ( 24 ). ( C ) and ( D ) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical ( n = 8667) and poised ( n = 3505) enhancers were used for further cluster analyses. ( E and F ) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).
Figure Legend Snippet: Dose dependent largazole effects on the epigenetic features of distal enhancer elements. ( A and B ) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) ( 23 ), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) ( 24 ). ( C ) and ( D ) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical ( n = 8667) and poised ( n = 3505) enhancers were used for further cluster analyses. ( E and F ) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).

Techniques Used: Chromatin Immunoprecipitation, Isolation, Activation Assay

Distinct H3K9 and H3K27 hyperacetylation responsive patterns upon largazole treatment. ( A ) A representative genomic snapshot of H3K27ac peaks illustrating different responses of gene bodies to newly acetylated histones. The signal initiates from the TSS (red dotted rectangle) of the FAT1 gene (orange panel) and spreads into the coding region or as in the case of CYP4V2 (purple panel), the preexisting acetylated TSS remains unmodified throughout all largazole dose treatments. Genes that do not show H3K9 or –K27 acetylation at the TSS (green panel) under basal conditions do not associate with the two histone marks as a result of largazole treatment. ( B ) Number of gene regions associated with the three response categories for H3K27ac (left) and H3K9ac (right). ( C ) Venn diagram showing the number of genes that exhibit new association with H3K27ac (green), H3K9ac (purple), and those that display both acetylation marks.
Figure Legend Snippet: Distinct H3K9 and H3K27 hyperacetylation responsive patterns upon largazole treatment. ( A ) A representative genomic snapshot of H3K27ac peaks illustrating different responses of gene bodies to newly acetylated histones. The signal initiates from the TSS (red dotted rectangle) of the FAT1 gene (orange panel) and spreads into the coding region or as in the case of CYP4V2 (purple panel), the preexisting acetylated TSS remains unmodified throughout all largazole dose treatments. Genes that do not show H3K9 or –K27 acetylation at the TSS (green panel) under basal conditions do not associate with the two histone marks as a result of largazole treatment. ( B ) Number of gene regions associated with the three response categories for H3K27ac (left) and H3K9ac (right). ( C ) Venn diagram showing the number of genes that exhibit new association with H3K27ac (green), H3K9ac (purple), and those that display both acetylation marks.

Techniques Used:

35) Product Images from "Activation of Mir-29a in Activated Hepatic Stellate Cells Modulates Its Profibrogenic Phenotype through Inhibition of Histone Deacetylases 4"

Article Title: Activation of Mir-29a in Activated Hepatic Stellate Cells Modulates Its Profibrogenic Phenotype through Inhibition of Histone Deacetylases 4

Journal: PLoS ONE

doi: 10.1371/journal.pone.0136453

Overexpression of miR-29a increased histone H3 at lysine 9 (H3K9Ac) and decreased Smad3 expression in HSCs. A miR-29a mimic and HDAC4 RNAi significantly increased H3K9Ac and decreased both Smad3 and p-Smad3 expression in HSCs of WT mice. Data are expressed as the mean ± SE of four independent experiments. *indicates a p
Figure Legend Snippet: Overexpression of miR-29a increased histone H3 at lysine 9 (H3K9Ac) and decreased Smad3 expression in HSCs. A miR-29a mimic and HDAC4 RNAi significantly increased H3K9Ac and decreased both Smad3 and p-Smad3 expression in HSCs of WT mice. Data are expressed as the mean ± SE of four independent experiments. *indicates a p

Techniques Used: Over Expression, Expressing, Mouse Assay

36) Product Images from "The Carboxyl Terminus of Rtt109 Functions in Chaperone Control of Histone Acetylation"

Article Title: The Carboxyl Terminus of Rtt109 Functions in Chaperone Control of Histone Acetylation

Journal: Eukaryotic Cell

doi: 10.1128/EC.00291-12

The carboxyl terminus of fungal Rtt109s contain a Lys/Arg-rich sequence which is essential for H3K9ac in S. cerevisiae . (A) Using the ClustalW algorithm, S. cerevisiae Rtt109 was aligned with predicted Rtt109 sequences from fungi of the Ascomycota , Basidiomycota
Figure Legend Snippet: The carboxyl terminus of fungal Rtt109s contain a Lys/Arg-rich sequence which is essential for H3K9ac in S. cerevisiae . (A) Using the ClustalW algorithm, S. cerevisiae Rtt109 was aligned with predicted Rtt109 sequences from fungi of the Ascomycota , Basidiomycota

Techniques Used: Sequencing

Lysine 290 of Rtt109 is important for in vivo H3K56ac and H3K9ac. (A) 12MYC-RTT109K290Q rtt109 Δ and 12MYC-RTT109K290R rtt109 Δ strains show significantly decreased levels of H3K9ac but not H3K56ac in vivo . Western blotting was performed
Figure Legend Snippet: Lysine 290 of Rtt109 is important for in vivo H3K56ac and H3K9ac. (A) 12MYC-RTT109K290Q rtt109 Δ and 12MYC-RTT109K290R rtt109 Δ strains show significantly decreased levels of H3K9ac but not H3K56ac in vivo . Western blotting was performed

Techniques Used: In Vivo, Western Blot

37) Product Images from "The Carboxyl Terminus of Rtt109 Functions in Chaperone Control of Histone Acetylation"

Article Title: The Carboxyl Terminus of Rtt109 Functions in Chaperone Control of Histone Acetylation

Journal: Eukaryotic Cell

doi: 10.1128/EC.00291-12

The carboxyl terminus of fungal Rtt109s contain a Lys/Arg-rich sequence which is essential for H3K9ac in S. cerevisiae . (A) Using the ClustalW algorithm, S. cerevisiae Rtt109 was aligned with predicted Rtt109 sequences from fungi of the Ascomycota , Basidiomycota
Figure Legend Snippet: The carboxyl terminus of fungal Rtt109s contain a Lys/Arg-rich sequence which is essential for H3K9ac in S. cerevisiae . (A) Using the ClustalW algorithm, S. cerevisiae Rtt109 was aligned with predicted Rtt109 sequences from fungi of the Ascomycota , Basidiomycota

Techniques Used: Sequencing

Lysine 290 of Rtt109 is important for in vivo H3K56ac and H3K9ac. (A) 12MYC-RTT109K290Q rtt109 Δ and 12MYC-RTT109K290R rtt109 Δ strains show significantly decreased levels of H3K9ac but not H3K56ac in vivo . Western blotting was performed
Figure Legend Snippet: Lysine 290 of Rtt109 is important for in vivo H3K56ac and H3K9ac. (A) 12MYC-RTT109K290Q rtt109 Δ and 12MYC-RTT109K290R rtt109 Δ strains show significantly decreased levels of H3K9ac but not H3K56ac in vivo . Western blotting was performed

Techniques Used: In Vivo, Western Blot

38) Product Images from "Foxa1 Functions as a Pioneer Transcription Factor at Transposable Elements to Activate Afp during Differentiation of Embryonic Stem Cells *"

Article Title: Foxa1 Functions as a Pioneer Transcription Factor at Transposable Elements to Activate Afp during Differentiation of Embryonic Stem Cells *

Journal: The Journal of Biological Chemistry

doi: 10.1074/jbc.M109.088096

Foxa1 acts upstream of Smads to mediate Smad binding, nucleosome occupancy reduction, and H3K9 acetylation. Chromatin immunoprecipitation was performed on ES cells treated with RA for 4 days and transfected with either Foxa1-targeted or scrambled siRNA oligos ( A , C , and H ) or treated with SB431542 or dimethyl sulfoxide ( B , F , and I ). Transfection of the siRNA oligos for Foxa1 or for a non-target control and treatment with SB431542 or dimethyl sulfoxide occurred coincident with addition of RA. DNA from immunoprecipitations for H3 ( A and B ), Foxa1, P-Smad2, and Smad4 ( C , D , and F ), and H3 and H3K9ac ( E and G–I ) was analyzed by real time PCR for binding to the Afp distal promoter. DNA from immunoprecipitations was analyzed by real time PCR for binding to the Afp distal promoter. Levels of acH3K9 are expressed as a ratio to levels of histone H3, determined by a separate immunoprecipitation. Error bars represent S.D. from at least three repetitions. ns , not significant.
Figure Legend Snippet: Foxa1 acts upstream of Smads to mediate Smad binding, nucleosome occupancy reduction, and H3K9 acetylation. Chromatin immunoprecipitation was performed on ES cells treated with RA for 4 days and transfected with either Foxa1-targeted or scrambled siRNA oligos ( A , C , and H ) or treated with SB431542 or dimethyl sulfoxide ( B , F , and I ). Transfection of the siRNA oligos for Foxa1 or for a non-target control and treatment with SB431542 or dimethyl sulfoxide occurred coincident with addition of RA. DNA from immunoprecipitations for H3 ( A and B ), Foxa1, P-Smad2, and Smad4 ( C , D , and F ), and H3 and H3K9ac ( E and G–I ) was analyzed by real time PCR for binding to the Afp distal promoter. DNA from immunoprecipitations was analyzed by real time PCR for binding to the Afp distal promoter. Levels of acH3K9 are expressed as a ratio to levels of histone H3, determined by a separate immunoprecipitation. Error bars represent S.D. from at least three repetitions. ns , not significant.

Techniques Used: Binding Assay, Chromatin Immunoprecipitation, Transfection, Real-time Polymerase Chain Reaction, Immunoprecipitation

39) Product Images from "A hit‐and‐run heat shock factor governs sustained histone methylation and transcriptional stress memory"

Article Title: A hit‐and‐run heat shock factor governs sustained histone methylation and transcriptional stress memory

Journal: The EMBO Journal

doi: 10.15252/embj.201592593

Histone H3K9ac profiles after ACC in Col‐0 and hsfa2 at HSP 18.2 , HSP 22.0 , HSP 70, and APX 2 as detected by Ch IP ‐ qPCR
Figure Legend Snippet: Histone H3K9ac profiles after ACC in Col‐0 and hsfa2 at HSP 18.2 , HSP 22.0 , HSP 70, and APX 2 as detected by Ch IP ‐ qPCR

Techniques Used: Real-time Polymerase Chain Reaction

40) Product Images from "A novel histone fold domain-containing protein that replaces TAF6 in Drosophila SAGA is required for SAGA-dependent gene expression"

Article Title: A novel histone fold domain-containing protein that replaces TAF6 in Drosophila SAGA is required for SAGA-dependent gene expression

Journal: Genes & Development

doi: 10.1101/gad.1846409

( A ) Histones were acid-extracted from wild-type (OregonR) or saf6 second instar larvae and analyzed by Western blotting using antibodies against ubH2B, H2B, H3K9ac, H3K14ac, H3K18ac, H3K23ac, or H3. (*) Cross-reactive band. ( B ) Quantitative PCR was performed
Figure Legend Snippet: ( A ) Histones were acid-extracted from wild-type (OregonR) or saf6 second instar larvae and analyzed by Western blotting using antibodies against ubH2B, H2B, H3K9ac, H3K14ac, H3K18ac, H3K23ac, or H3. (*) Cross-reactive band. ( B ) Quantitative PCR was performed

Techniques Used: Western Blot, Real-time Polymerase Chain Reaction

Related Articles

other:

Article Title: The Carboxyl Terminus of Rtt109 Functions in Chaperone Control of Histone Acetylation
Article Snippet: Additionally, as expected, 6×HIS-Rtt109 with either 6×HIS-Vps75 or 6×HIS-Asf1 catalyzed H3K56ac while 6×HIS-Rtt109 and 6×HIS-Vps75 also catalyzed H3K9ac ( ).

Article Title: Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers
Article Snippet: Specifically, we observe loss of H3K27ac but not H3K9ac with higher doses of largazole (Figure and ).

Article Title: Analysis of Histones H3 and H4 Reveals Novel and Conserved Post-Translational Modifications in Sugarcane
Article Snippet: Immunoblot analysis indicates that H3K4me1, H3K4me3, H3K9me2, H3K27me3 and H3K9ac, modifications previously identified by nanoLC-MS/MS, are indeed present in sugarcane histones from leaves and stems.

Expressing:

Article Title: Coordinate Changes in Histone Modifications, mRNA Levels, and Metabolite Profiles in Clonal INS-1 832/13 ?-Cells Accompany Functional Adaptations to Lipotoxicity *
Article Snippet: .. As expected, we found that genes showing increased expression in response to lipotoxicity, e.g. Insig1, Lss, Idi1 , Hmgcs1 , and Peci , also exhibited an increased fold-enrichment of H3K9Ac and/or H3K79me2. ..

ChIP-sequencing:

Article Title: Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers
Article Snippet: .. H3K9ac and H3K27ac The FStitch algorithm ( ) was used to identify genomic regions enriched with H3K9ac and –K27ac signal from HCT116 ChIP-seq experiments. .. In order to acquire uniform FStitch signal calls across experiments targeting the same acetylated lysine, we determined the minimal number of unique reads found in datasets for H3K9ac as well as in those for H3K27ac ( ).

In Vitro:

Article Title: The Carboxyl Terminus of Rtt109 Functions in Chaperone Control of Histone Acetylation
Article Snippet: .. In vitro , however, in the presence of Vps75, Rtt109(1–424) appears to catalyze H3K9ac as efficiently as full-length Rtt109 ( ). .. These data could be described by the model if Asf1 has an inhibitory role on Rtt109-mediated H3K9ac and if Rtt109C, in addition to Vps75, is required to overcome the inhibition.

Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 92
    Abcam h3k9ac
    Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in <t>H3K9ac</t> and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.
    H3k9ac, supplied by Abcam, used in various techniques. Bioz Stars score: 92/100, based on 96 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/h3k9ac/product/Abcam
    Average 92 stars, based on 96 article reviews
    Price from $9.99 to $1999.99
    h3k9ac - by Bioz Stars, 2020-05
    92/100 stars
      Buy from Supplier

    85
    Abcam h3k9ac upstate
    Profile of histone marks and CTCF with tandem repeats. Histone modification and CTCF binding profile are shown at different genomic coordinates with the tandem repeats. ( A ) Different kinds of tandem repeats present next to each other are shown in the Y chromosome. Two big tandem repeats are numbered as 1 and 2. Tandem repeat 1 does not show any enrichment with the tested antibodies whereas repeat 2 is enriched with <t>H3K9ac</t> and CTCF. There are few more tandem repeats on the right side of the tandem repeat 2, which does not show enrichment with any of the tested antibodies. ( B ) Multiple tandem repeats associated with the PLCXD1 gene (blue line with arrow) have been shown with the histone modification and CTCF binding profile. Tandem repeats have been marked in the figure as 1, 2 and 3. Tandem repeat-3 enriches with anti-H3K9ac and anti-CTCF, tandem repeat-2 does not enrich with any of the tested antibodies whereas repeat-1 is enriched with anti-H3K9ac and anti-H3K27me3.
    H3k9ac Upstate, supplied by Abcam, used in various techniques. Bioz Stars score: 85/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/h3k9ac upstate/product/Abcam
    Average 85 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    h3k9ac upstate - by Bioz Stars, 2020-05
    85/100 stars
      Buy from Supplier

    Image Search Results


    Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in H3K9ac and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.

    Journal: Nucleic Acids Research

    Article Title: Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers

    doi: 10.1093/nar/gkx1225

    Figure Lengend Snippet: Dose-dependent cellular and histone acetylation responses to largazole treatment in HCT116 cells. ( A ) Quantitative analysis of the cell cycle progression by propidium iodide staining using flow cytometry in HCT116 cells treated with the indicted largazole concentration for 25 h. ( B ) Histogram showing the percentages of cells in G1 (red), S (blue), and G2 (yellow) phases of the cell cycle as well as subG1 fraction (green). ( C ) Dose-dependent global changes in indicated histone marks upon largazole exposure for 16 h as determined by immunoblotting with antibodies against each histone mark. Total histone H3 was used as a loading control. ( D and E ) Changes in H3K9ac and H3K27ac induced by largazole according to genomic territories. Pie charts illustrate the distribution of H3K9ac and H3K27ac signals (as determined by FStitch) from ChIP-seq experiments in vehicle (DMSO) treated HCT116 cells. Genomic territories are divided by gene bodies (purple), enhancer regions (green), TSS (blue), intergenic locations (orange) and 3′ ends (red). ( F and G ) The log 2 fold change ratio for increasing H3K9ac and H3K27ac in each genomic territory with various doses of largazole (nM) exposure.

    Article Snippet: Specifically, we observe loss of H3K27ac but not H3K9ac with higher doses of largazole (Figure and ).

    Techniques: Staining, Flow Cytometry, Cytometry, Concentration Assay, Chromatin Immunoprecipitation

    Dose dependent largazole effects on the epigenetic features of distal enhancer elements. ( A and B ) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) ( 23 ), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) ( 24 ). ( C ) and ( D ) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical ( n = 8667) and poised ( n = 3505) enhancers were used for further cluster analyses. ( E and F ) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).

    Journal: Nucleic Acids Research

    Article Title: Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers

    doi: 10.1093/nar/gkx1225

    Figure Lengend Snippet: Dose dependent largazole effects on the epigenetic features of distal enhancer elements. ( A and B ) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) ( 23 ), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) ( 24 ). ( C ) and ( D ) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical ( n = 8667) and poised ( n = 3505) enhancers were used for further cluster analyses. ( E and F ) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).

    Article Snippet: Specifically, we observe loss of H3K27ac but not H3K9ac with higher doses of largazole (Figure and ).

    Techniques: Chromatin Immunoprecipitation, Isolation, Activation Assay

    Distinct H3K9 and H3K27 hyperacetylation responsive patterns upon largazole treatment. ( A ) A representative genomic snapshot of H3K27ac peaks illustrating different responses of gene bodies to newly acetylated histones. The signal initiates from the TSS (red dotted rectangle) of the FAT1 gene (orange panel) and spreads into the coding region or as in the case of CYP4V2 (purple panel), the preexisting acetylated TSS remains unmodified throughout all largazole dose treatments. Genes that do not show H3K9 or –K27 acetylation at the TSS (green panel) under basal conditions do not associate with the two histone marks as a result of largazole treatment. ( B ) Number of gene regions associated with the three response categories for H3K27ac (left) and H3K9ac (right). ( C ) Venn diagram showing the number of genes that exhibit new association with H3K27ac (green), H3K9ac (purple), and those that display both acetylation marks.

    Journal: Nucleic Acids Research

    Article Title: Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers

    doi: 10.1093/nar/gkx1225

    Figure Lengend Snippet: Distinct H3K9 and H3K27 hyperacetylation responsive patterns upon largazole treatment. ( A ) A representative genomic snapshot of H3K27ac peaks illustrating different responses of gene bodies to newly acetylated histones. The signal initiates from the TSS (red dotted rectangle) of the FAT1 gene (orange panel) and spreads into the coding region or as in the case of CYP4V2 (purple panel), the preexisting acetylated TSS remains unmodified throughout all largazole dose treatments. Genes that do not show H3K9 or –K27 acetylation at the TSS (green panel) under basal conditions do not associate with the two histone marks as a result of largazole treatment. ( B ) Number of gene regions associated with the three response categories for H3K27ac (left) and H3K9ac (right). ( C ) Venn diagram showing the number of genes that exhibit new association with H3K27ac (green), H3K9ac (purple), and those that display both acetylation marks.

    Article Snippet: Specifically, we observe loss of H3K27ac but not H3K9ac with higher doses of largazole (Figure and ).

    Techniques:

    Distribution patterns of histone post-translational modifications in sugarcane. (A) Immunoblot analysis of global histone H3 modifications in sugarcane tissues. (B) Sub-nuclear localization of H3K4me1, H3K4me3, H3K9me2, H3K27me3 and H3K9ac. (C) Chromatin distribution of sugarcane and Arabidopsis; white arrows show DAPI densely stained regions in sugarcane, representing heterochromatic blocks. In Arabidopsis, the chromocenters are well defined regions of heterochromatin (yellow arrows). (D) H3T3ph (red signals) does not co-localize with actively transcribed regions rich in RNA Polymerase II (green signals). Instead, it appears to be associated with silent chromatin; DAPI densely stained regions (grey nucleus, blue arrows) coincide with H3T3ph brighter foci (red nucleus, blue arrows), whereas weaker/absent H3T3ph regions (red nucleus, orange arrows) coincide with the less condensed chromatin poorly stained with DAPI (grey nucleus, orange arrows). Bars = 5 μm.

    Journal: PLoS ONE

    Article Title: Analysis of Histones H3 and H4 Reveals Novel and Conserved Post-Translational Modifications in Sugarcane

    doi: 10.1371/journal.pone.0134586

    Figure Lengend Snippet: Distribution patterns of histone post-translational modifications in sugarcane. (A) Immunoblot analysis of global histone H3 modifications in sugarcane tissues. (B) Sub-nuclear localization of H3K4me1, H3K4me3, H3K9me2, H3K27me3 and H3K9ac. (C) Chromatin distribution of sugarcane and Arabidopsis; white arrows show DAPI densely stained regions in sugarcane, representing heterochromatic blocks. In Arabidopsis, the chromocenters are well defined regions of heterochromatin (yellow arrows). (D) H3T3ph (red signals) does not co-localize with actively transcribed regions rich in RNA Polymerase II (green signals). Instead, it appears to be associated with silent chromatin; DAPI densely stained regions (grey nucleus, blue arrows) coincide with H3T3ph brighter foci (red nucleus, blue arrows), whereas weaker/absent H3T3ph regions (red nucleus, orange arrows) coincide with the less condensed chromatin poorly stained with DAPI (grey nucleus, orange arrows). Bars = 5 μm.

    Article Snippet: Immunoblot analysis indicates that H3K4me1, H3K4me3, H3K9me2, H3K27me3 and H3K9ac, modifications previously identified by nanoLC-MS/MS, are indeed present in sugarcane histones from leaves and stems.

    Techniques: Staining

    Repressive histone modifications following GATA-1 overexpression in AML-ELs. ChIP at the PU . 1 gene locus was carried out for the H3K9Me3, H3K27Me3, and H3K9Ac histone tail modifications in OCI-M2 (left) and K562 (right) cells. Grey bars: control cells, dark bars: 48hrs after GATA-1 transgene transfection. Data are relative to control antibody IPs (Y axis). T-test significance: p

    Journal: PLoS ONE

    Article Title: GATA-1 Inhibits PU.1 Gene via DNA and Histone H3K9 Methylation of Its Distal Enhancer in Erythroleukemia

    doi: 10.1371/journal.pone.0152234

    Figure Lengend Snippet: Repressive histone modifications following GATA-1 overexpression in AML-ELs. ChIP at the PU . 1 gene locus was carried out for the H3K9Me3, H3K27Me3, and H3K9Ac histone tail modifications in OCI-M2 (left) and K562 (right) cells. Grey bars: control cells, dark bars: 48hrs after GATA-1 transgene transfection. Data are relative to control antibody IPs (Y axis). T-test significance: p

    Article Snippet: IP-antibodies: GATA-1 (N6/sc265-Santa Cruz, USA), PU.1 (sc352-Santa Cruz, USA), DNMT1 (Ab13537-Abcam, UK), H3K9Ac (07-352-Upstate, USA), H3K9Me3 (Ab88-98-Abcam, UK), H3K4Me3 (pAb003-050-Diagenode, Belgium), H3K27Me3 (Ab6002-Abcam, UK), and control antibody (NI01-EMB Biosciences, USA).

    Techniques: Over Expression, Chromatin Immunoprecipitation, Transfection

    Profile of histone marks and CTCF with tandem repeats. Histone modification and CTCF binding profile are shown at different genomic coordinates with the tandem repeats. ( A ) Different kinds of tandem repeats present next to each other are shown in the Y chromosome. Two big tandem repeats are numbered as 1 and 2. Tandem repeat 1 does not show any enrichment with the tested antibodies whereas repeat 2 is enriched with H3K9ac and CTCF. There are few more tandem repeats on the right side of the tandem repeat 2, which does not show enrichment with any of the tested antibodies. ( B ) Multiple tandem repeats associated with the PLCXD1 gene (blue line with arrow) have been shown with the histone modification and CTCF binding profile. Tandem repeats have been marked in the figure as 1, 2 and 3. Tandem repeat-3 enriches with anti-H3K9ac and anti-CTCF, tandem repeat-2 does not enrich with any of the tested antibodies whereas repeat-1 is enriched with anti-H3K9ac and anti-H3K27me3.

    Journal: Nucleic Acids Research

    Article Title: Epigenetic profile of the euchromatic region of human Y chromosome

    doi: 10.1093/nar/gkq1342

    Figure Lengend Snippet: Profile of histone marks and CTCF with tandem repeats. Histone modification and CTCF binding profile are shown at different genomic coordinates with the tandem repeats. ( A ) Different kinds of tandem repeats present next to each other are shown in the Y chromosome. Two big tandem repeats are numbered as 1 and 2. Tandem repeat 1 does not show any enrichment with the tested antibodies whereas repeat 2 is enriched with H3K9ac and CTCF. There are few more tandem repeats on the right side of the tandem repeat 2, which does not show enrichment with any of the tested antibodies. ( B ) Multiple tandem repeats associated with the PLCXD1 gene (blue line with arrow) have been shown with the histone modification and CTCF binding profile. Tandem repeats have been marked in the figure as 1, 2 and 3. Tandem repeat-3 enriches with anti-H3K9ac and anti-CTCF, tandem repeat-2 does not enrich with any of the tested antibodies whereas repeat-1 is enriched with anti-H3K9ac and anti-H3K27me3.

    Article Snippet: Then ChIP was done using H3K9Me3 (Upstate), H3K9ac (Upstate), H3K27Me3 (Upstate) and CTCF (Abcam) antibodies on WBCs of two different individuals, 8 experiments in total.

    Techniques: Modification, Binding Assay

    Pattern of H3K9ac and H3K9me3 at DAZ gene loci. It shows DAZ gene, a duplicated gene with conflicting histone marks. The figure shows two copies of the DAZ gene, DAZ3 and DAZ4 present in opposite directions and the pattern of H3K9ac and H3K9me3 marks. Both alleles show almost equal enrichment of H3K9ac and H3K9me3 at their transcriptional start site.

    Journal: Nucleic Acids Research

    Article Title: Epigenetic profile of the euchromatic region of human Y chromosome

    doi: 10.1093/nar/gkq1342

    Figure Lengend Snippet: Pattern of H3K9ac and H3K9me3 at DAZ gene loci. It shows DAZ gene, a duplicated gene with conflicting histone marks. The figure shows two copies of the DAZ gene, DAZ3 and DAZ4 present in opposite directions and the pattern of H3K9ac and H3K9me3 marks. Both alleles show almost equal enrichment of H3K9ac and H3K9me3 at their transcriptional start site.

    Article Snippet: Then ChIP was done using H3K9Me3 (Upstate), H3K9ac (Upstate), H3K27Me3 (Upstate) and CTCF (Abcam) antibodies on WBCs of two different individuals, 8 experiments in total.

    Techniques:

    Association of histone marks with different sequences of the Y chromosome. ( A ) Features of the Y chromosome are shown on the top, telomere, centromere and heterochromatin (black), and euchromatin. Different kinds of sequences in euchromatin are represented as colored blocks on the chromosome, blue (pseudoautosomal region), green (X-degenerate), red (X-transposed) and yellow (ampliconic). To visualize the data clearly, both enriched and not enriched regions have been shown for H3K9me3, H3K9ac and H3K27me3 histone modifications in dark red, blue and orange, respectively (the same convention has been followed in all the other figures also). We observe a specific global pattern of histone marks in different classes of sequences—the pseudoautosomal region is predominately enriched with H3K9ac, the X transposed is enriched with H3K9me3, the X-degenerate region shows almost equal enrichment with all marks and the ampliconic regions show a low enrichment with all histone marks, H3K9me3 being the most enriched. ( B ) Here we show the average enrichment of histone marks in different classes of sequences distributed along the chromosome. As visually observed in Figure 1 A, different classes of sequences have a global pattern of histone marks. The pattern of histone marks in different class of sequences followed the visual observation except in the case of X-degenerate region. In visual analysis X-degenerate is enriched equally with H3K9me3 and H3K9ac but when we calculated average enrichment in different region we found that H3K9ac is more enriched than H3K9me3. In the given table, each class of sequences, from short (p) and long (q) arm are clubbed together to simplify the table.

    Journal: Nucleic Acids Research

    Article Title: Epigenetic profile of the euchromatic region of human Y chromosome

    doi: 10.1093/nar/gkq1342

    Figure Lengend Snippet: Association of histone marks with different sequences of the Y chromosome. ( A ) Features of the Y chromosome are shown on the top, telomere, centromere and heterochromatin (black), and euchromatin. Different kinds of sequences in euchromatin are represented as colored blocks on the chromosome, blue (pseudoautosomal region), green (X-degenerate), red (X-transposed) and yellow (ampliconic). To visualize the data clearly, both enriched and not enriched regions have been shown for H3K9me3, H3K9ac and H3K27me3 histone modifications in dark red, blue and orange, respectively (the same convention has been followed in all the other figures also). We observe a specific global pattern of histone marks in different classes of sequences—the pseudoautosomal region is predominately enriched with H3K9ac, the X transposed is enriched with H3K9me3, the X-degenerate region shows almost equal enrichment with all marks and the ampliconic regions show a low enrichment with all histone marks, H3K9me3 being the most enriched. ( B ) Here we show the average enrichment of histone marks in different classes of sequences distributed along the chromosome. As visually observed in Figure 1 A, different classes of sequences have a global pattern of histone marks. The pattern of histone marks in different class of sequences followed the visual observation except in the case of X-degenerate region. In visual analysis X-degenerate is enriched equally with H3K9me3 and H3K9ac but when we calculated average enrichment in different region we found that H3K9ac is more enriched than H3K9me3. In the given table, each class of sequences, from short (p) and long (q) arm are clubbed together to simplify the table.

    Article Snippet: Then ChIP was done using H3K9Me3 (Upstate), H3K9ac (Upstate), H3K27Me3 (Upstate) and CTCF (Abcam) antibodies on WBCs of two different individuals, 8 experiments in total.

    Techniques:

    Epigenetic pattern of SRY gene. Co-ordinates of the SRY gene in the chromosome are given above in the figure while the gene body has been shown below. The genomic CpG island and the clone use to analyse the methylation status of the island are shown below the gene. We see a high enrichment of H3K9me3 at the start site and in the body of the gene, while H3K9ac and H3K27me3 are enriched from the body of the gene to upstream of the gene. A very clean enrichment of CTCF was seen at the CpG island upstream of the gene.

    Journal: Nucleic Acids Research

    Article Title: Epigenetic profile of the euchromatic region of human Y chromosome

    doi: 10.1093/nar/gkq1342

    Figure Lengend Snippet: Epigenetic pattern of SRY gene. Co-ordinates of the SRY gene in the chromosome are given above in the figure while the gene body has been shown below. The genomic CpG island and the clone use to analyse the methylation status of the island are shown below the gene. We see a high enrichment of H3K9me3 at the start site and in the body of the gene, while H3K9ac and H3K27me3 are enriched from the body of the gene to upstream of the gene. A very clean enrichment of CTCF was seen at the CpG island upstream of the gene.

    Article Snippet: Then ChIP was done using H3K9Me3 (Upstate), H3K9ac (Upstate), H3K27Me3 (Upstate) and CTCF (Abcam) antibodies on WBCs of two different individuals, 8 experiments in total.

    Techniques: Methylation