h3k4me1  (Cell Signaling Technology Inc)


Bioz Verified Symbol Cell Signaling Technology Inc is a verified supplier
Bioz Manufacturer Symbol Cell Signaling Technology Inc manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 95

    Structured Review

    Cell Signaling Technology Inc h3k4me1
    H3k4me1, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/h3k4me1/product/Cell Signaling Technology Inc
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    h3k4me1 - by Bioz Stars, 2023-02
    95/100 stars

    Images

    h3k4me1  (Cell Signaling Technology Inc)


    Bioz Verified Symbol Cell Signaling Technology Inc is a verified supplier
    Bioz Manufacturer Symbol Cell Signaling Technology Inc manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 95

    Structured Review

    Cell Signaling Technology Inc h3k4me1
    H3k4me1, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/h3k4me1/product/Cell Signaling Technology Inc
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    h3k4me1 - by Bioz Stars, 2023-02
    95/100 stars

    Images

    rabbit polyclonal anti h3k4me1 antibody  (Cell Signaling Technology Inc)


    Bioz Verified Symbol Cell Signaling Technology Inc is a verified supplier
    Bioz Manufacturer Symbol Cell Signaling Technology Inc manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 95

    Structured Review

    Cell Signaling Technology Inc rabbit polyclonal anti h3k4me1 antibody
    p40 supplementation in early life stimulates short-term up-regulation of Setd1b gene expression, but sustained increase in epigenetic marks in mice. The treatment plans for detecting the short-term ( <xref ref-type=Figure 3 A ) and long-term effects ( Figure 3 B ) are described. ( A and B ) RNA was isolated from colonic tissues for RT-PCR analysis of Setd1b gene expression. Each symbol represents one mouse in A and B . ( C ) Paraffin-embedded tissue sections were prepared for immunohistochemistry using anti-H3K4me1 antibody and fluorescein isothiocyanate–conjugated secondary antibody (green), an epithelial cell marker using anti–E-cadherin antibody and Cy3-conjugated secondary antibody (red), and nuclei using 4′,6-diamidino-2-phenylindole (DAPI) staining (blue). Images were taken using a fluorescent microscope at 40×. ( D ) The numbers of H3K4me1 and E-cadherin double-positive cells per crypt are shown. N = 5 in each group. " width="250" height="auto" />
    Rabbit Polyclonal Anti H3k4me1 Antibody, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rabbit polyclonal anti h3k4me1 antibody/product/Cell Signaling Technology Inc
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    rabbit polyclonal anti h3k4me1 antibody - by Bioz Stars, 2023-02
    95/100 stars

    Images

    1) Product Images from "Exposure to p40 in Early Life Prevents Intestinal Inflammation in Adulthood Through Inducing a Long-Lasting Epigenetic Imprint on TGFβ"

    Article Title: Exposure to p40 in Early Life Prevents Intestinal Inflammation in Adulthood Through Inducing a Long-Lasting Epigenetic Imprint on TGFβ

    Journal: Cellular and Molecular Gastroenterology and Hepatology

    doi: 10.1016/j.jcmgh.2021.01.004

    p40 supplementation in early life stimulates short-term up-regulation of Setd1b gene expression, but sustained increase in epigenetic marks in mice. The treatment plans for detecting the short-term ( <xref ref-type=Figure 3 A ) and long-term effects ( Figure 3 B ) are described. ( A and B ) RNA was isolated from colonic tissues for RT-PCR analysis of Setd1b gene expression. Each symbol represents one mouse in A and B . ( C ) Paraffin-embedded tissue sections were prepared for immunohistochemistry using anti-H3K4me1 antibody and fluorescein isothiocyanate–conjugated secondary antibody (green), an epithelial cell marker using anti–E-cadherin antibody and Cy3-conjugated secondary antibody (red), and nuclei using 4′,6-diamidino-2-phenylindole (DAPI) staining (blue). Images were taken using a fluorescent microscope at 40×. ( D ) The numbers of H3K4me1 and E-cadherin double-positive cells per crypt are shown. N = 5 in each group. " title="... Paraffin-embedded tissue sections were prepared for immunohistochemistry using anti-H3K4me1 antibody and fluorescein isothiocyanate–conjugated secondary antibody (green), an ..." property="contentUrl" width="100%" height="100%"/>
    Figure Legend Snippet: p40 supplementation in early life stimulates short-term up-regulation of Setd1b gene expression, but sustained increase in epigenetic marks in mice. The treatment plans for detecting the short-term ( Figure 3 A ) and long-term effects ( Figure 3 B ) are described. ( A and B ) RNA was isolated from colonic tissues for RT-PCR analysis of Setd1b gene expression. Each symbol represents one mouse in A and B . ( C ) Paraffin-embedded tissue sections were prepared for immunohistochemistry using anti-H3K4me1 antibody and fluorescein isothiocyanate–conjugated secondary antibody (green), an epithelial cell marker using anti–E-cadherin antibody and Cy3-conjugated secondary antibody (red), and nuclei using 4′,6-diamidino-2-phenylindole (DAPI) staining (blue). Images were taken using a fluorescent microscope at 40×. ( D ) The numbers of H3K4me1 and E-cadherin double-positive cells per crypt are shown. N = 5 in each group.

    Techniques Used: Expressing, Isolation, Reverse Transcription Polymerase Chain Reaction, Immunohistochemistry, Marker, Staining, Microscopy

    h3k4me1  (Cell Signaling Technology Inc)


    Bioz Verified Symbol Cell Signaling Technology Inc is a verified supplier
    Bioz Manufacturer Symbol Cell Signaling Technology Inc manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 95

    Structured Review

    Cell Signaling Technology Inc h3k4me1
    Rcor2 inhibits Dppa3 and Dazl expression by enhancing H3K9me3 on their promoters. (a) The protein level of <t>H3K4me1</t> and H3K9me3 in WT and Rcor2 −/− mESCs. (b, e) Diagrams of the tested regions by ChIP-qPCR on Dppa3 (b) and Dazl (e) genes and basal H3K9me3 level on Dppa3 (b) and Dazl (e) genes in mESCs (data from GEO: GSM32218, generated by ENCODE ). (c, f) ChIP-qPCR shows the enrichment of Rcor2 on Dppa3 (c) and Dazl (f) promoters at the tested regions, relative to their respective negative control regions, which are located in gene bodies (not shown). Data are expressed as mean ± SEM, n = 3, ∗ p < 0.05. (d, g) ChIP-qPCR shows the H3K9me3 level at the tested regions of Dppa3 (d) and Dazl (g) genes in WT and Rcor2 −/− mESCs. Data are expressed as mean ± SEM, n = 3, ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001.
    H3k4me1, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/h3k4me1/product/Cell Signaling Technology Inc
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    h3k4me1 - by Bioz Stars, 2023-02
    95/100 stars

    Images

    1) Product Images from "Rcor2 Is Required for Somatic Differentiation and Represses Germline Cell Fate"

    Article Title: Rcor2 Is Required for Somatic Differentiation and Represses Germline Cell Fate

    Journal: Stem Cells International

    doi: 10.1155/2022/5283615

    Rcor2 inhibits Dppa3 and Dazl expression by enhancing H3K9me3 on their promoters. (a) The protein level of H3K4me1 and H3K9me3 in WT and Rcor2 −/− mESCs. (b, e) Diagrams of the tested regions by ChIP-qPCR on Dppa3 (b) and Dazl (e) genes and basal H3K9me3 level on Dppa3 (b) and Dazl (e) genes in mESCs (data from GEO: GSM32218, generated by ENCODE ). (c, f) ChIP-qPCR shows the enrichment of Rcor2 on Dppa3 (c) and Dazl (f) promoters at the tested regions, relative to their respective negative control regions, which are located in gene bodies (not shown). Data are expressed as mean ± SEM, n = 3, ∗ p < 0.05. (d, g) ChIP-qPCR shows the H3K9me3 level at the tested regions of Dppa3 (d) and Dazl (g) genes in WT and Rcor2 −/− mESCs. Data are expressed as mean ± SEM, n = 3, ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001.
    Figure Legend Snippet: Rcor2 inhibits Dppa3 and Dazl expression by enhancing H3K9me3 on their promoters. (a) The protein level of H3K4me1 and H3K9me3 in WT and Rcor2 −/− mESCs. (b, e) Diagrams of the tested regions by ChIP-qPCR on Dppa3 (b) and Dazl (e) genes and basal H3K9me3 level on Dppa3 (b) and Dazl (e) genes in mESCs (data from GEO: GSM32218, generated by ENCODE ). (c, f) ChIP-qPCR shows the enrichment of Rcor2 on Dppa3 (c) and Dazl (f) promoters at the tested regions, relative to their respective negative control regions, which are located in gene bodies (not shown). Data are expressed as mean ± SEM, n = 3, ∗ p < 0.05. (d, g) ChIP-qPCR shows the H3K9me3 level at the tested regions of Dppa3 (d) and Dazl (g) genes in WT and Rcor2 −/− mESCs. Data are expressed as mean ± SEM, n = 3, ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001.

    Techniques Used: Expressing, Generated, Negative Control

    h3k4me1  (Cell Signaling Technology Inc)


    Bioz Verified Symbol Cell Signaling Technology Inc is a verified supplier
    Bioz Manufacturer Symbol Cell Signaling Technology Inc manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 95

    Structured Review

    Cell Signaling Technology Inc h3k4me1
    Information of Reagents and Antibodies
    H3k4me1, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/h3k4me1/product/Cell Signaling Technology Inc
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    h3k4me1 - by Bioz Stars, 2023-02
    95/100 stars

    Images

    1) Product Images from "KDM6A Regulates Cell Plasticity and Pancreatic Cancer Progression by Noncanonical Activin Pathway"

    Article Title: KDM6A Regulates Cell Plasticity and Pancreatic Cancer Progression by Noncanonical Activin Pathway

    Journal: Cellular and Molecular Gastroenterology and Hepatology

    doi: 10.1016/j.jcmgh.2021.09.014

    Information of Reagents and Antibodies
    Figure Legend Snippet: Information of Reagents and Antibodies

    Techniques Used: Concentration Assay, Enzyme-linked Immunosorbent Assay

    anti h3k4me1  (Cell Signaling Technology Inc)


    Bioz Verified Symbol Cell Signaling Technology Inc is a verified supplier
    Bioz Manufacturer Symbol Cell Signaling Technology Inc manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 95

    Structured Review

    Cell Signaling Technology Inc anti h3k4me1
    H2A.Z forms a complex with KDM1A, <t>H3K4me1</t> and H3K4me2. A Western blot analysis revealed that H2A.Z is mainly expressed in the nucleus in HuccT-1 and RBE cells. B Immunofluorescence (IF) analysis of the nuclear localization of H2A.Z in HuccT-1 and RBE cells (400 × magnification). C Western blot analysis revealed that H2A.Z is mainly expressed in the nucleus in HuccT-1 and RBE cells with H2A.Z silencing. E Endogenous KDM1A, H3K4me1 and H3K4me2 were precipitated with the anti-H2A.Z antibody in HuccT-1, RBE and HIBEpic cells. F Western blot analysis revealed that KDM1A silencing can increase the relative level of SFRP1 expression
    Anti H3k4me1, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/anti h3k4me1/product/Cell Signaling Technology Inc
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    anti h3k4me1 - by Bioz Stars, 2023-02
    95/100 stars

    Images

    1) Product Images from "The H2A.Z-KDM1A complex promotes tumorigenesis by localizing in the nucleus to promote SFRP1 promoter methylation in cholangiocarcinoma cells"

    Article Title: The H2A.Z-KDM1A complex promotes tumorigenesis by localizing in the nucleus to promote SFRP1 promoter methylation in cholangiocarcinoma cells

    Journal: BMC Cancer

    doi: 10.1186/s12885-022-10279-y

    H2A.Z forms a complex with KDM1A, H3K4me1 and H3K4me2. A Western blot analysis revealed that H2A.Z is mainly expressed in the nucleus in HuccT-1 and RBE cells. B Immunofluorescence (IF) analysis of the nuclear localization of H2A.Z in HuccT-1 and RBE cells (400 × magnification). C Western blot analysis revealed that H2A.Z is mainly expressed in the nucleus in HuccT-1 and RBE cells with H2A.Z silencing. E Endogenous KDM1A, H3K4me1 and H3K4me2 were precipitated with the anti-H2A.Z antibody in HuccT-1, RBE and HIBEpic cells. F Western blot analysis revealed that KDM1A silencing can increase the relative level of SFRP1 expression
    Figure Legend Snippet: H2A.Z forms a complex with KDM1A, H3K4me1 and H3K4me2. A Western blot analysis revealed that H2A.Z is mainly expressed in the nucleus in HuccT-1 and RBE cells. B Immunofluorescence (IF) analysis of the nuclear localization of H2A.Z in HuccT-1 and RBE cells (400 × magnification). C Western blot analysis revealed that H2A.Z is mainly expressed in the nucleus in HuccT-1 and RBE cells with H2A.Z silencing. E Endogenous KDM1A, H3K4me1 and H3K4me2 were precipitated with the anti-H2A.Z antibody in HuccT-1, RBE and HIBEpic cells. F Western blot analysis revealed that KDM1A silencing can increase the relative level of SFRP1 expression

    Techniques Used: Western Blot, Immunofluorescence, Expressing

    H2A.Z binds to the upstream region of the SFRP1 promoter and reduces SFRP1 expression. A Graphical representation of the CpG sites in the SFRP1 promoter. B ChIP assay of KDM1A, H3K4me1 and H3K4me2 enrichment in the P3 region upstream of the SFRP1 promoter. IgG was used as the negative control. Relative fold enrichment = [%(ChIP/Input)]/[%(IgG/Input)]. C BSP analysis of the CpG site methylation rate. Each dot represents one CpG site. White represents the absence of methylation, and pale green to deep yellow represent increasing methylation rates. D Quantitative RT–PCR analysis of the SFRP1 mRNA transcript level relative to the GAPDH mRNA transcript level in the blank control, LV-shRNA-NC, LV-shR-H2A.Z and LV-NC-H2A.Z + 5-aza-dC groups. The data are expressed as the individual mean values or the mean ± SD of each group in three independent experiments. ** p < 0.01, *** p < 0.001
    Figure Legend Snippet: H2A.Z binds to the upstream region of the SFRP1 promoter and reduces SFRP1 expression. A Graphical representation of the CpG sites in the SFRP1 promoter. B ChIP assay of KDM1A, H3K4me1 and H3K4me2 enrichment in the P3 region upstream of the SFRP1 promoter. IgG was used as the negative control. Relative fold enrichment = [%(ChIP/Input)]/[%(IgG/Input)]. C BSP analysis of the CpG site methylation rate. Each dot represents one CpG site. White represents the absence of methylation, and pale green to deep yellow represent increasing methylation rates. D Quantitative RT–PCR analysis of the SFRP1 mRNA transcript level relative to the GAPDH mRNA transcript level in the blank control, LV-shRNA-NC, LV-shR-H2A.Z and LV-NC-H2A.Z + 5-aza-dC groups. The data are expressed as the individual mean values or the mean ± SD of each group in three independent experiments. ** p < 0.01, *** p < 0.001

    Techniques Used: Expressing, Negative Control, Methylation, Quantitative RT-PCR, shRNA

    Schematic illustration of the role of H2A.Z in regulating SFRP1 promoter activity in ICC. In the nucleus, H2A.Z recruits KDM1A, H3K4me1 and H3K4me2 to form a complex to promote demethylation upstream of the SFRP1 promoter and coordinates with HP1α, which is located at downstream CpG islands and recruits SUV39H1/H3K9me3/DNMTs to repress SFRP1 transcription
    Figure Legend Snippet: Schematic illustration of the role of H2A.Z in regulating SFRP1 promoter activity in ICC. In the nucleus, H2A.Z recruits KDM1A, H3K4me1 and H3K4me2 to form a complex to promote demethylation upstream of the SFRP1 promoter and coordinates with HP1α, which is located at downstream CpG islands and recruits SUV39H1/H3K9me3/DNMTs to repress SFRP1 transcription

    Techniques Used: Activity Assay

    h3k4me1  (Cell Signaling Technology Inc)


    Bioz Verified Symbol Cell Signaling Technology Inc is a verified supplier
    Bioz Manufacturer Symbol Cell Signaling Technology Inc manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 95

    Structured Review

    Cell Signaling Technology Inc h3k4me1
    ( A ) NCI-H526 cell lines transduced with either nontargeting CRISPR sgRNA or C11orf53-specific sgRNAs for 4 days. The protein levels of C11orf53, <t>H3K4me1,</t> H3K4me3, H3K27me3, and H3K27ac levels were determined by Western blot. Total histone H3 was used as internal control. The average plot shows the total H3K27ac ( B ), and H3K4me1 ( C ) peaks in NCI-H526 cell lines transduced with either nontargeting CRISPR sgRNA or C11orf53-specific sgRNAs. Chromatin from Drosophila S2 cells (10%) was used as spike-in. IgG, immunoglubulin G. ( D ) The log 2 fold-change heatmap shows the loss of H3K4me1 and H3K27ac signal at C11ORF53 peaks after C11ORF53 depletion. ( E ) Histone H3K27ac signals from ChIP-seq identifies putative SEs in NCI-H526 cells transduced with either nontargeting CRISPR sgRNA (top) or two distinct C11orf53-specific sgRNAs (middle and bottom). Hockey-stick plot representing the normalized rank and signals of H3K27ac. Representative of top-ranked SE-associated genes from each group are labeled. aa, amino acids. ( F ) Representative track examples have shown the H3K27ac levels at SOX9, GFI1B, and PTGS1 gene loci in cells transduced with either CRISPR sgRNA or C11orf53-specific sgRNAs. ( G ) The Venn diagram shows the overlap between ATAC-seq peaks and C11orf53 peaks in NCI-H526 cells. ( H ) The average plot shows the ATAC-seq signal between cells transduced with either CRISPR sgRNA or C11orf53-specific sgRNAs. The group 1 peaks are ATAC-seq/C11orf53 common peaks. Group 2 peaks are ATAC-seq alone peaks. ( I ) Representative tracks showing ATAC-seq peaks at GFI1B gene loci in cells transduced with either CRISPR sgRNA or C11orf53-specific sgRNAs.
    H3k4me1, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/h3k4me1/product/Cell Signaling Technology Inc
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    h3k4me1 - by Bioz Stars, 2023-02
    95/100 stars

    Images

    1) Product Images from "POU2AF2/C11orf53 functions as a coactivator of POU2F3 by maintaining chromatin accessibility and enhancer activity"

    Article Title: POU2AF2/C11orf53 functions as a coactivator of POU2F3 by maintaining chromatin accessibility and enhancer activity

    Journal: Science Advances

    doi: 10.1126/sciadv.abq2403

    ( A ) NCI-H526 cell lines transduced with either nontargeting CRISPR sgRNA or C11orf53-specific sgRNAs for 4 days. The protein levels of C11orf53, H3K4me1, H3K4me3, H3K27me3, and H3K27ac levels were determined by Western blot. Total histone H3 was used as internal control. The average plot shows the total H3K27ac ( B ), and H3K4me1 ( C ) peaks in NCI-H526 cell lines transduced with either nontargeting CRISPR sgRNA or C11orf53-specific sgRNAs. Chromatin from Drosophila S2 cells (10%) was used as spike-in. IgG, immunoglubulin G. ( D ) The log 2 fold-change heatmap shows the loss of H3K4me1 and H3K27ac signal at C11ORF53 peaks after C11ORF53 depletion. ( E ) Histone H3K27ac signals from ChIP-seq identifies putative SEs in NCI-H526 cells transduced with either nontargeting CRISPR sgRNA (top) or two distinct C11orf53-specific sgRNAs (middle and bottom). Hockey-stick plot representing the normalized rank and signals of H3K27ac. Representative of top-ranked SE-associated genes from each group are labeled. aa, amino acids. ( F ) Representative track examples have shown the H3K27ac levels at SOX9, GFI1B, and PTGS1 gene loci in cells transduced with either CRISPR sgRNA or C11orf53-specific sgRNAs. ( G ) The Venn diagram shows the overlap between ATAC-seq peaks and C11orf53 peaks in NCI-H526 cells. ( H ) The average plot shows the ATAC-seq signal between cells transduced with either CRISPR sgRNA or C11orf53-specific sgRNAs. The group 1 peaks are ATAC-seq/C11orf53 common peaks. Group 2 peaks are ATAC-seq alone peaks. ( I ) Representative tracks showing ATAC-seq peaks at GFI1B gene loci in cells transduced with either CRISPR sgRNA or C11orf53-specific sgRNAs.
    Figure Legend Snippet: ( A ) NCI-H526 cell lines transduced with either nontargeting CRISPR sgRNA or C11orf53-specific sgRNAs for 4 days. The protein levels of C11orf53, H3K4me1, H3K4me3, H3K27me3, and H3K27ac levels were determined by Western blot. Total histone H3 was used as internal control. The average plot shows the total H3K27ac ( B ), and H3K4me1 ( C ) peaks in NCI-H526 cell lines transduced with either nontargeting CRISPR sgRNA or C11orf53-specific sgRNAs. Chromatin from Drosophila S2 cells (10%) was used as spike-in. IgG, immunoglubulin G. ( D ) The log 2 fold-change heatmap shows the loss of H3K4me1 and H3K27ac signal at C11ORF53 peaks after C11ORF53 depletion. ( E ) Histone H3K27ac signals from ChIP-seq identifies putative SEs in NCI-H526 cells transduced with either nontargeting CRISPR sgRNA (top) or two distinct C11orf53-specific sgRNAs (middle and bottom). Hockey-stick plot representing the normalized rank and signals of H3K27ac. Representative of top-ranked SE-associated genes from each group are labeled. aa, amino acids. ( F ) Representative track examples have shown the H3K27ac levels at SOX9, GFI1B, and PTGS1 gene loci in cells transduced with either CRISPR sgRNA or C11orf53-specific sgRNAs. ( G ) The Venn diagram shows the overlap between ATAC-seq peaks and C11orf53 peaks in NCI-H526 cells. ( H ) The average plot shows the ATAC-seq signal between cells transduced with either CRISPR sgRNA or C11orf53-specific sgRNAs. The group 1 peaks are ATAC-seq/C11orf53 common peaks. Group 2 peaks are ATAC-seq alone peaks. ( I ) Representative tracks showing ATAC-seq peaks at GFI1B gene loci in cells transduced with either CRISPR sgRNA or C11orf53-specific sgRNAs.

    Techniques Used: Transduction, CRISPR, Western Blot, ChIP-sequencing, Labeling

    h3k4me1  (Cell Signaling Technology Inc)


    Bioz Verified Symbol Cell Signaling Technology Inc is a verified supplier
    Bioz Manufacturer Symbol Cell Signaling Technology Inc manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 95

    Structured Review

    Cell Signaling Technology Inc h3k4me1
    Endogenous MBD5 and MBD6 are stable components in the BAP1 complex. A HEK293T cells were infected by lentivirus expressing GFP, GFP-tagged MBD5, or GFP-tagged-MBD6. The protein levels of GFP, GFP-MBD5, and GFP-MBD6 were determined by western blot, n =2. B The GFP-fusion proteins were purified from HEK293T cells stably expressing GFP, GFP-MBD5, or GFP-MBD6 defined in A . The purified proteins were subjected to mass spectrometry analysis. Peptide numbers of subunits within the BAP1 complex pulled down by GFP-tagged proteins are shown. C Immunoprecipitation (IP) of endogenous BAP1 from HEK293T cells followed by immunoblot (IB) for BAP1, MBD5, and MBD6. IgG was used as a negative control, n = 2. D IP of endogenous MBD5 or MBD6 from HEK293T cells followed by IB for MBD5, MBD6, BAP1, ASXL1, and ASXL2. IgG was used as a negative control, n = 2. E Nuclear extract from HEK293T cells was subjected to size exclusion (SE) chromatography and then protein levels of BAP1, MBD5, and MBD6 were determined by western blot analysis, n = 2. F The average plots shown represent the chromatin occupancy of H3K27Ac, <t>H3K4me1,</t> H3K4me3, and H3K27me3 centered on MBD5 peaks ( F ) or MBD6 peaks ( G ). H Sorted and centered heatmaps generated from ChIP-seq data analyses show the occupancy of BAP1, MBD5, and MBD6 in HEK293T cells. All rows are centered on BAP1 peaks based on the ranking of signals. I The average plot shows the co-occupancy between BAP1, MBD5, and MBD6 centered on BAP1 peaks. J The representative tracks show H3K27Ac, H3K4me1, and H3K4me3 levels at BAP1, MBD5, and MBD6 occupied loci in HEK293T cells. K A Venn diagram representation of the overlapped ChIP-seq peaks between BAP1, MBD5, and MBD6
    H3k4me1, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/h3k4me1/product/Cell Signaling Technology Inc
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    h3k4me1 - by Bioz Stars, 2023-02
    95/100 stars

    Images

    1) Product Images from "MBD5 and MBD6 stabilize the BAP1 complex and promote BAP1-dependent cancer"

    Article Title: MBD5 and MBD6 stabilize the BAP1 complex and promote BAP1-dependent cancer

    Journal: Genome Biology

    doi: 10.1186/s13059-022-02776-x

    Endogenous MBD5 and MBD6 are stable components in the BAP1 complex. A HEK293T cells were infected by lentivirus expressing GFP, GFP-tagged MBD5, or GFP-tagged-MBD6. The protein levels of GFP, GFP-MBD5, and GFP-MBD6 were determined by western blot, n =2. B The GFP-fusion proteins were purified from HEK293T cells stably expressing GFP, GFP-MBD5, or GFP-MBD6 defined in A . The purified proteins were subjected to mass spectrometry analysis. Peptide numbers of subunits within the BAP1 complex pulled down by GFP-tagged proteins are shown. C Immunoprecipitation (IP) of endogenous BAP1 from HEK293T cells followed by immunoblot (IB) for BAP1, MBD5, and MBD6. IgG was used as a negative control, n = 2. D IP of endogenous MBD5 or MBD6 from HEK293T cells followed by IB for MBD5, MBD6, BAP1, ASXL1, and ASXL2. IgG was used as a negative control, n = 2. E Nuclear extract from HEK293T cells was subjected to size exclusion (SE) chromatography and then protein levels of BAP1, MBD5, and MBD6 were determined by western blot analysis, n = 2. F The average plots shown represent the chromatin occupancy of H3K27Ac, H3K4me1, H3K4me3, and H3K27me3 centered on MBD5 peaks ( F ) or MBD6 peaks ( G ). H Sorted and centered heatmaps generated from ChIP-seq data analyses show the occupancy of BAP1, MBD5, and MBD6 in HEK293T cells. All rows are centered on BAP1 peaks based on the ranking of signals. I The average plot shows the co-occupancy between BAP1, MBD5, and MBD6 centered on BAP1 peaks. J The representative tracks show H3K27Ac, H3K4me1, and H3K4me3 levels at BAP1, MBD5, and MBD6 occupied loci in HEK293T cells. K A Venn diagram representation of the overlapped ChIP-seq peaks between BAP1, MBD5, and MBD6
    Figure Legend Snippet: Endogenous MBD5 and MBD6 are stable components in the BAP1 complex. A HEK293T cells were infected by lentivirus expressing GFP, GFP-tagged MBD5, or GFP-tagged-MBD6. The protein levels of GFP, GFP-MBD5, and GFP-MBD6 were determined by western blot, n =2. B The GFP-fusion proteins were purified from HEK293T cells stably expressing GFP, GFP-MBD5, or GFP-MBD6 defined in A . The purified proteins were subjected to mass spectrometry analysis. Peptide numbers of subunits within the BAP1 complex pulled down by GFP-tagged proteins are shown. C Immunoprecipitation (IP) of endogenous BAP1 from HEK293T cells followed by immunoblot (IB) for BAP1, MBD5, and MBD6. IgG was used as a negative control, n = 2. D IP of endogenous MBD5 or MBD6 from HEK293T cells followed by IB for MBD5, MBD6, BAP1, ASXL1, and ASXL2. IgG was used as a negative control, n = 2. E Nuclear extract from HEK293T cells was subjected to size exclusion (SE) chromatography and then protein levels of BAP1, MBD5, and MBD6 were determined by western blot analysis, n = 2. F The average plots shown represent the chromatin occupancy of H3K27Ac, H3K4me1, H3K4me3, and H3K27me3 centered on MBD5 peaks ( F ) or MBD6 peaks ( G ). H Sorted and centered heatmaps generated from ChIP-seq data analyses show the occupancy of BAP1, MBD5, and MBD6 in HEK293T cells. All rows are centered on BAP1 peaks based on the ranking of signals. I The average plot shows the co-occupancy between BAP1, MBD5, and MBD6 centered on BAP1 peaks. J The representative tracks show H3K27Ac, H3K4me1, and H3K4me3 levels at BAP1, MBD5, and MBD6 occupied loci in HEK293T cells. K A Venn diagram representation of the overlapped ChIP-seq peaks between BAP1, MBD5, and MBD6

    Techniques Used: Infection, Expressing, Western Blot, Purification, Stable Transfection, Mass Spectrometry, Immunoprecipitation, Negative Control, Chromatography, Generated, ChIP-sequencing

    Characterization of MBD6 occupancy in SCLC cells. A The representative tracks show chromatin occupancy of MBD6, ASXL1/2/3, and BAP1 binding sites in the human SCLC cell line NCI-H1963. B The bar plot shows the feature distribution of MBD6, ASXL1/2/3, and BAP1 peaks in NCI-H1963 cells. C Sorted and centered heatmaps generated from ChIP-seq and ATAC-seq data analyses show the occupancy of MBD6, ASXL1/2/3, BAP1, H3K27Ac, H3K4me1, H3K4me3, and H3K27me3 in NCI-H1963 cells. All signals were centered on MBD6 peaks, which were classified into three clusters, based on k-means clustering according to MBD6, H3K4me1, H3K4me3, and H3K27Ac ChIP-seq. D Representative tracks showing the occupancy MBD6, BAP1, ASXL1-3, and histone marks. E Pathway analysis was performed using ChIPseeker with genes nearest to MBD6 three cluster peaks defined in C . F Motif enrichment analysis of MBD6 three clusters’ peaks defined in C from NCI-H1963 cells. G The box plot shows the log2-fold-change of H3K4me1, H3K4me3, and H3K27Ac signals versus input at MBD6/BAP1/ASXL1, MBD6/BAP1/ASXL2, or MBD6/BAP1/ASXL3 co-occupied genomic regions
    Figure Legend Snippet: Characterization of MBD6 occupancy in SCLC cells. A The representative tracks show chromatin occupancy of MBD6, ASXL1/2/3, and BAP1 binding sites in the human SCLC cell line NCI-H1963. B The bar plot shows the feature distribution of MBD6, ASXL1/2/3, and BAP1 peaks in NCI-H1963 cells. C Sorted and centered heatmaps generated from ChIP-seq and ATAC-seq data analyses show the occupancy of MBD6, ASXL1/2/3, BAP1, H3K27Ac, H3K4me1, H3K4me3, and H3K27me3 in NCI-H1963 cells. All signals were centered on MBD6 peaks, which were classified into three clusters, based on k-means clustering according to MBD6, H3K4me1, H3K4me3, and H3K27Ac ChIP-seq. D Representative tracks showing the occupancy MBD6, BAP1, ASXL1-3, and histone marks. E Pathway analysis was performed using ChIPseeker with genes nearest to MBD6 three cluster peaks defined in C . F Motif enrichment analysis of MBD6 three clusters’ peaks defined in C from NCI-H1963 cells. G The box plot shows the log2-fold-change of H3K4me1, H3K4me3, and H3K27Ac signals versus input at MBD6/BAP1/ASXL1, MBD6/BAP1/ASXL2, or MBD6/BAP1/ASXL3 co-occupied genomic regions

    Techniques Used: Binding Assay, Generated, ChIP-sequencing

    h3k4me1  (Cell Signaling Technology Inc)


    Bioz Verified Symbol Cell Signaling Technology Inc is a verified supplier
    Bioz Manufacturer Symbol Cell Signaling Technology Inc manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 95

    Structured Review

    Cell Signaling Technology Inc h3k4me1
    a Pie chart depicting the intersection of regions with increased accessibility under LSS by ATAC-Seq, with KLF4 and BRG1 ChIP-Seq data from PAEC transduced with caMEK5. Percentages indicate the fraction of DAR with increased accessibility under LSS vs ST that are differentially enriched for KLF4 and/or BRG1. b Scatterplot showing the correlation between KLF4 binding and accessibility changes at LSS vs ST DAR co-occupied by KLF4-BRG1. Indicated values were calculated by a two-tailed Pearson R test, with P < 0.0001. c ATAC-Seq and KLF4 and BRG1 ChIP-Seq tracks showing enrichment for both factors at the DAR 39 Kb upstream of DUSP5 . d PAEC were treated with siRNA targeting BRG1 (siBRG1) or with non-targeting controls (siC) prior to exposure to 15 dyn/cm 2 of LSS or ST conditions for 24 h. Bar graphs indicate accessibility of the DAR 39 Kb upstream of DUSP5 , and DUSP5 gene expression, both assessed by qPCR. e Venn diagram showing the percentage of KLF4-BRG1 co-occupied DAR with increased accessibility under LSS, that are enriched for <t>H3K4me1</t> and H3K27ac. n = 2 experimental replicates for a – c , e , and n = 4 experimental replicates for d. Data are shown as the mean ± s.e.m. P values were determined by Student’s two-tailed t -test. Source data are provided as a Source Data file.
    H3k4me1, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/h3k4me1/product/Cell Signaling Technology Inc
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    h3k4me1 - by Bioz Stars, 2023-02
    95/100 stars

    Images

    1) Product Images from "KLF4 recruits SWI/SNF to increase chromatin accessibility and reprogram the endothelial enhancer landscape under laminar shear stress"

    Article Title: KLF4 recruits SWI/SNF to increase chromatin accessibility and reprogram the endothelial enhancer landscape under laminar shear stress

    Journal: Nature Communications

    doi: 10.1038/s41467-022-32566-9

    a Pie chart depicting the intersection of regions with increased accessibility under LSS by ATAC-Seq, with KLF4 and BRG1 ChIP-Seq data from PAEC transduced with caMEK5. Percentages indicate the fraction of DAR with increased accessibility under LSS vs ST that are differentially enriched for KLF4 and/or BRG1. b Scatterplot showing the correlation between KLF4 binding and accessibility changes at LSS vs ST DAR co-occupied by KLF4-BRG1. Indicated values were calculated by a two-tailed Pearson R test, with P < 0.0001. c ATAC-Seq and KLF4 and BRG1 ChIP-Seq tracks showing enrichment for both factors at the DAR 39 Kb upstream of DUSP5 . d PAEC were treated with siRNA targeting BRG1 (siBRG1) or with non-targeting controls (siC) prior to exposure to 15 dyn/cm 2 of LSS or ST conditions for 24 h. Bar graphs indicate accessibility of the DAR 39 Kb upstream of DUSP5 , and DUSP5 gene expression, both assessed by qPCR. e Venn diagram showing the percentage of KLF4-BRG1 co-occupied DAR with increased accessibility under LSS, that are enriched for H3K4me1 and H3K27ac. n = 2 experimental replicates for a – c , e , and n = 4 experimental replicates for d. Data are shown as the mean ± s.e.m. P values were determined by Student’s two-tailed t -test. Source data are provided as a Source Data file.
    Figure Legend Snippet: a Pie chart depicting the intersection of regions with increased accessibility under LSS by ATAC-Seq, with KLF4 and BRG1 ChIP-Seq data from PAEC transduced with caMEK5. Percentages indicate the fraction of DAR with increased accessibility under LSS vs ST that are differentially enriched for KLF4 and/or BRG1. b Scatterplot showing the correlation between KLF4 binding and accessibility changes at LSS vs ST DAR co-occupied by KLF4-BRG1. Indicated values were calculated by a two-tailed Pearson R test, with P < 0.0001. c ATAC-Seq and KLF4 and BRG1 ChIP-Seq tracks showing enrichment for both factors at the DAR 39 Kb upstream of DUSP5 . d PAEC were treated with siRNA targeting BRG1 (siBRG1) or with non-targeting controls (siC) prior to exposure to 15 dyn/cm 2 of LSS or ST conditions for 24 h. Bar graphs indicate accessibility of the DAR 39 Kb upstream of DUSP5 , and DUSP5 gene expression, both assessed by qPCR. e Venn diagram showing the percentage of KLF4-BRG1 co-occupied DAR with increased accessibility under LSS, that are enriched for H3K4me1 and H3K27ac. n = 2 experimental replicates for a – c , e , and n = 4 experimental replicates for d. Data are shown as the mean ± s.e.m. P values were determined by Student’s two-tailed t -test. Source data are provided as a Source Data file.

    Techniques Used: ChIP-sequencing, Transduction, Binding Assay, Two Tailed Test, Expressing

    h3k4me  (Cell Signaling Technology Inc)


    Bioz Verified Symbol Cell Signaling Technology Inc is a verified supplier
    Bioz Manufacturer Symbol Cell Signaling Technology Inc manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 95

    Structured Review

    Cell Signaling Technology Inc h3k4me
    H3k4me, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/h3k4me/product/Cell Signaling Technology Inc
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    h3k4me - by Bioz Stars, 2023-02
    95/100 stars

    Images

    h3k27ac  (Cell Signaling Technology Inc)


    Bioz Verified Symbol Cell Signaling Technology Inc is a verified supplier
    Bioz Manufacturer Symbol Cell Signaling Technology Inc manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 95

    Structured Review

    Cell Signaling Technology Inc h3k27ac
    A. SMARCB1 CUT & RUN following expression of SMARCB1 in G401 RT cells for 24 h identifies 94,114 SMARCB1 peaks. Genomic binding signal from SMARCB1- and GFP-induced G401 (SB1, GFP) cells is sorted by SMARCB1 enrichment and clustered by genomic elements defined by chromatin marks generated from MNase-ChIP. Traditional enhancers (TEs, black) and super enhancers (SEs, gold) were called by using <t>H3K27Ac</t> data from SB1 cells according to Rank Ordering of Super Enhancers (ROSE). Promoter-associated peaks outside a ROSE-defined enhancer (Ps, green) were called within 1 kb of an H3K4me3-enriched promoter. Primed enhancer sites (PEs, dark blue) are H3K4me1-enriched, H3K27Ac-negative regions >1 kb from the nearest TSS. Data shown are the average of two biological replicates. B-G. BRD9, SMARCA4, and SMARCB1 genomic binding data from 15,471 differentially bound BRD9 CUT & RUN peaks (SB1 vs. GFP, FDR < 0.05). BRD9 CUT & RUN data are the average of 3 biological replicates. B-D BRD9, SMARCA4, and SMARCB1 genomic binding data from 13,410 sites with significant increase in BRD9 upon SMARCB1 expression (SB1 vs. GFP, FDR < 0.05) (B). Sites gaining BRD9 are annotated with ROSE and histone modification data analysis from SMARCB1-induced G401 cells (C). Circle graphs show the percentage of BRD9-up sites bound by SMARCB1 (D). E-G. BRD9, SMARCA4, and SMARCB1 genomic binding data from 2,061 sites with a significant decrease in BRD9 (SB1 vs. GFP, FDR < 0.05) (E). Sites losing BRD9 are annotated with ROSE and histone modification data analysis from GFP-induced (negative control) G401 cells (F). Sites >1 kb from a TSS with no H3K4me1 were classified as TSS-distal sites (TDs). A black box indicates a region within TEs, SEs, and Ps where SMARCA4 is also lost upon SMARCB1 rescue (E, F). Circle graphs show the percentage of BRD9-down sites bound by SMARCB1 (G). H. Linear regression comparing SMARCB1-dependent changes in accessibility to fold-change BRD9 enrichment between SMARCB1 (SB1)- and GFP-induced G401 cells at sites where SMARCB1 and BRD9 were detected in at least one sample at a differentially accessible region (SMARCB1 + /BRD9 + Differentially Accessible Regions). SMARCB1 + /BRD9 + differentially accessible regions are correlated with SMARCB1-dependent changes in BRD9 binding (p<0.0001, R 2 =0.66). I. Genomic heatmaps of ATAC-seq data, SMARCB1 and BRD9 CUT & RUN, and SMARCA4 ChIP-seq at the sites from (H) that are bound by SMARCB1 and BRD9 that show SMARCB1-dependent changes in ATAC accessibility, centered on the differentially accessible nucleosome-free regions. Sites are sorted by difference in the ATAC-seq nucleosome-free signal measured between SMARCB1 (SB1)- and GFP-induced G401 cells. The red sidebar indicates ATAC-up sites. The blue sidebar indicates ATAC-down sites.
    H3k27ac, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/h3k27ac/product/Cell Signaling Technology Inc
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    h3k27ac - by Bioz Stars, 2023-02
    95/100 stars

    Images

    1) Product Images from "Functional interplay between SWI/SNF complexes underlies BRD9 dependency in SMARCB1-mutant cancers"

    Article Title: Functional interplay between SWI/SNF complexes underlies BRD9 dependency in SMARCB1-mutant cancers

    Journal: bioRxiv

    doi: 10.1101/2022.08.07.503080

    A. SMARCB1 CUT & RUN following expression of SMARCB1 in G401 RT cells for 24 h identifies 94,114 SMARCB1 peaks. Genomic binding signal from SMARCB1- and GFP-induced G401 (SB1, GFP) cells is sorted by SMARCB1 enrichment and clustered by genomic elements defined by chromatin marks generated from MNase-ChIP. Traditional enhancers (TEs, black) and super enhancers (SEs, gold) were called by using H3K27Ac data from SB1 cells according to Rank Ordering of Super Enhancers (ROSE). Promoter-associated peaks outside a ROSE-defined enhancer (Ps, green) were called within 1 kb of an H3K4me3-enriched promoter. Primed enhancer sites (PEs, dark blue) are H3K4me1-enriched, H3K27Ac-negative regions >1 kb from the nearest TSS. Data shown are the average of two biological replicates. B-G. BRD9, SMARCA4, and SMARCB1 genomic binding data from 15,471 differentially bound BRD9 CUT & RUN peaks (SB1 vs. GFP, FDR < 0.05). BRD9 CUT & RUN data are the average of 3 biological replicates. B-D BRD9, SMARCA4, and SMARCB1 genomic binding data from 13,410 sites with significant increase in BRD9 upon SMARCB1 expression (SB1 vs. GFP, FDR < 0.05) (B). Sites gaining BRD9 are annotated with ROSE and histone modification data analysis from SMARCB1-induced G401 cells (C). Circle graphs show the percentage of BRD9-up sites bound by SMARCB1 (D). E-G. BRD9, SMARCA4, and SMARCB1 genomic binding data from 2,061 sites with a significant decrease in BRD9 (SB1 vs. GFP, FDR < 0.05) (E). Sites losing BRD9 are annotated with ROSE and histone modification data analysis from GFP-induced (negative control) G401 cells (F). Sites >1 kb from a TSS with no H3K4me1 were classified as TSS-distal sites (TDs). A black box indicates a region within TEs, SEs, and Ps where SMARCA4 is also lost upon SMARCB1 rescue (E, F). Circle graphs show the percentage of BRD9-down sites bound by SMARCB1 (G). H. Linear regression comparing SMARCB1-dependent changes in accessibility to fold-change BRD9 enrichment between SMARCB1 (SB1)- and GFP-induced G401 cells at sites where SMARCB1 and BRD9 were detected in at least one sample at a differentially accessible region (SMARCB1 + /BRD9 + Differentially Accessible Regions). SMARCB1 + /BRD9 + differentially accessible regions are correlated with SMARCB1-dependent changes in BRD9 binding (p<0.0001, R 2 =0.66). I. Genomic heatmaps of ATAC-seq data, SMARCB1 and BRD9 CUT & RUN, and SMARCA4 ChIP-seq at the sites from (H) that are bound by SMARCB1 and BRD9 that show SMARCB1-dependent changes in ATAC accessibility, centered on the differentially accessible nucleosome-free regions. Sites are sorted by difference in the ATAC-seq nucleosome-free signal measured between SMARCB1 (SB1)- and GFP-induced G401 cells. The red sidebar indicates ATAC-up sites. The blue sidebar indicates ATAC-down sites.
    Figure Legend Snippet: A. SMARCB1 CUT & RUN following expression of SMARCB1 in G401 RT cells for 24 h identifies 94,114 SMARCB1 peaks. Genomic binding signal from SMARCB1- and GFP-induced G401 (SB1, GFP) cells is sorted by SMARCB1 enrichment and clustered by genomic elements defined by chromatin marks generated from MNase-ChIP. Traditional enhancers (TEs, black) and super enhancers (SEs, gold) were called by using H3K27Ac data from SB1 cells according to Rank Ordering of Super Enhancers (ROSE). Promoter-associated peaks outside a ROSE-defined enhancer (Ps, green) were called within 1 kb of an H3K4me3-enriched promoter. Primed enhancer sites (PEs, dark blue) are H3K4me1-enriched, H3K27Ac-negative regions >1 kb from the nearest TSS. Data shown are the average of two biological replicates. B-G. BRD9, SMARCA4, and SMARCB1 genomic binding data from 15,471 differentially bound BRD9 CUT & RUN peaks (SB1 vs. GFP, FDR < 0.05). BRD9 CUT & RUN data are the average of 3 biological replicates. B-D BRD9, SMARCA4, and SMARCB1 genomic binding data from 13,410 sites with significant increase in BRD9 upon SMARCB1 expression (SB1 vs. GFP, FDR < 0.05) (B). Sites gaining BRD9 are annotated with ROSE and histone modification data analysis from SMARCB1-induced G401 cells (C). Circle graphs show the percentage of BRD9-up sites bound by SMARCB1 (D). E-G. BRD9, SMARCA4, and SMARCB1 genomic binding data from 2,061 sites with a significant decrease in BRD9 (SB1 vs. GFP, FDR < 0.05) (E). Sites losing BRD9 are annotated with ROSE and histone modification data analysis from GFP-induced (negative control) G401 cells (F). Sites >1 kb from a TSS with no H3K4me1 were classified as TSS-distal sites (TDs). A black box indicates a region within TEs, SEs, and Ps where SMARCA4 is also lost upon SMARCB1 rescue (E, F). Circle graphs show the percentage of BRD9-down sites bound by SMARCB1 (G). H. Linear regression comparing SMARCB1-dependent changes in accessibility to fold-change BRD9 enrichment between SMARCB1 (SB1)- and GFP-induced G401 cells at sites where SMARCB1 and BRD9 were detected in at least one sample at a differentially accessible region (SMARCB1 + /BRD9 + Differentially Accessible Regions). SMARCB1 + /BRD9 + differentially accessible regions are correlated with SMARCB1-dependent changes in BRD9 binding (p<0.0001, R 2 =0.66). I. Genomic heatmaps of ATAC-seq data, SMARCB1 and BRD9 CUT & RUN, and SMARCA4 ChIP-seq at the sites from (H) that are bound by SMARCB1 and BRD9 that show SMARCB1-dependent changes in ATAC accessibility, centered on the differentially accessible nucleosome-free regions. Sites are sorted by difference in the ATAC-seq nucleosome-free signal measured between SMARCB1 (SB1)- and GFP-induced G401 cells. The red sidebar indicates ATAC-up sites. The blue sidebar indicates ATAC-down sites.

    Techniques Used: Expressing, Binding Assay, Generated, Modification, Negative Control, ChIP-sequencing

    Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 95
    Cell Signaling Technology Inc h3k4me1
    H3k4me1, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/h3k4me1/product/Cell Signaling Technology Inc
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    h3k4me1 - by Bioz Stars, 2023-02
    95/100 stars
      Buy from Supplier

    95
    Cell Signaling Technology Inc rabbit polyclonal anti h3k4me1 antibody
    p40 supplementation in early life stimulates short-term up-regulation of Setd1b gene expression, but sustained increase in epigenetic marks in mice. The treatment plans for detecting the short-term ( <xref ref-type=Figure 3 A ) and long-term effects ( Figure 3 B ) are described. ( A and B ) RNA was isolated from colonic tissues for RT-PCR analysis of Setd1b gene expression. Each symbol represents one mouse in A and B . ( C ) Paraffin-embedded tissue sections were prepared for immunohistochemistry using anti-H3K4me1 antibody and fluorescein isothiocyanate–conjugated secondary antibody (green), an epithelial cell marker using anti–E-cadherin antibody and Cy3-conjugated secondary antibody (red), and nuclei using 4′,6-diamidino-2-phenylindole (DAPI) staining (blue). Images were taken using a fluorescent microscope at 40×. ( D ) The numbers of H3K4me1 and E-cadherin double-positive cells per crypt are shown. N = 5 in each group. " width="250" height="auto" />
    Rabbit Polyclonal Anti H3k4me1 Antibody, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rabbit polyclonal anti h3k4me1 antibody/product/Cell Signaling Technology Inc
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    rabbit polyclonal anti h3k4me1 antibody - by Bioz Stars, 2023-02
    95/100 stars
      Buy from Supplier

    95
    Cell Signaling Technology Inc anti h3k4me1
    H2A.Z forms a complex with KDM1A, <t>H3K4me1</t> and H3K4me2. A Western blot analysis revealed that H2A.Z is mainly expressed in the nucleus in HuccT-1 and RBE cells. B Immunofluorescence (IF) analysis of the nuclear localization of H2A.Z in HuccT-1 and RBE cells (400 × magnification). C Western blot analysis revealed that H2A.Z is mainly expressed in the nucleus in HuccT-1 and RBE cells with H2A.Z silencing. E Endogenous KDM1A, H3K4me1 and H3K4me2 were precipitated with the anti-H2A.Z antibody in HuccT-1, RBE and HIBEpic cells. F Western blot analysis revealed that KDM1A silencing can increase the relative level of SFRP1 expression
    Anti H3k4me1, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/anti h3k4me1/product/Cell Signaling Technology Inc
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    anti h3k4me1 - by Bioz Stars, 2023-02
    95/100 stars
      Buy from Supplier

    95
    Cell Signaling Technology Inc h3k4me
    H2A.Z forms a complex with KDM1A, <t>H3K4me1</t> and H3K4me2. A Western blot analysis revealed that H2A.Z is mainly expressed in the nucleus in HuccT-1 and RBE cells. B Immunofluorescence (IF) analysis of the nuclear localization of H2A.Z in HuccT-1 and RBE cells (400 × magnification). C Western blot analysis revealed that H2A.Z is mainly expressed in the nucleus in HuccT-1 and RBE cells with H2A.Z silencing. E Endogenous KDM1A, H3K4me1 and H3K4me2 were precipitated with the anti-H2A.Z antibody in HuccT-1, RBE and HIBEpic cells. F Western blot analysis revealed that KDM1A silencing can increase the relative level of SFRP1 expression
    H3k4me, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/h3k4me/product/Cell Signaling Technology Inc
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    h3k4me - by Bioz Stars, 2023-02
    95/100 stars
      Buy from Supplier

    95
    Cell Signaling Technology Inc h3k27ac
    A. SMARCB1 CUT & RUN following expression of SMARCB1 in G401 RT cells for 24 h identifies 94,114 SMARCB1 peaks. Genomic binding signal from SMARCB1- and GFP-induced G401 (SB1, GFP) cells is sorted by SMARCB1 enrichment and clustered by genomic elements defined by chromatin marks generated from MNase-ChIP. Traditional enhancers (TEs, black) and super enhancers (SEs, gold) were called by using <t>H3K27Ac</t> data from SB1 cells according to Rank Ordering of Super Enhancers (ROSE). Promoter-associated peaks outside a ROSE-defined enhancer (Ps, green) were called within 1 kb of an H3K4me3-enriched promoter. Primed enhancer sites (PEs, dark blue) are H3K4me1-enriched, H3K27Ac-negative regions >1 kb from the nearest TSS. Data shown are the average of two biological replicates. B-G. BRD9, SMARCA4, and SMARCB1 genomic binding data from 15,471 differentially bound BRD9 CUT & RUN peaks (SB1 vs. GFP, FDR < 0.05). BRD9 CUT & RUN data are the average of 3 biological replicates. B-D BRD9, SMARCA4, and SMARCB1 genomic binding data from 13,410 sites with significant increase in BRD9 upon SMARCB1 expression (SB1 vs. GFP, FDR < 0.05) (B). Sites gaining BRD9 are annotated with ROSE and histone modification data analysis from SMARCB1-induced G401 cells (C). Circle graphs show the percentage of BRD9-up sites bound by SMARCB1 (D). E-G. BRD9, SMARCA4, and SMARCB1 genomic binding data from 2,061 sites with a significant decrease in BRD9 (SB1 vs. GFP, FDR < 0.05) (E). Sites losing BRD9 are annotated with ROSE and histone modification data analysis from GFP-induced (negative control) G401 cells (F). Sites >1 kb from a TSS with no H3K4me1 were classified as TSS-distal sites (TDs). A black box indicates a region within TEs, SEs, and Ps where SMARCA4 is also lost upon SMARCB1 rescue (E, F). Circle graphs show the percentage of BRD9-down sites bound by SMARCB1 (G). H. Linear regression comparing SMARCB1-dependent changes in accessibility to fold-change BRD9 enrichment between SMARCB1 (SB1)- and GFP-induced G401 cells at sites where SMARCB1 and BRD9 were detected in at least one sample at a differentially accessible region (SMARCB1 + /BRD9 + Differentially Accessible Regions). SMARCB1 + /BRD9 + differentially accessible regions are correlated with SMARCB1-dependent changes in BRD9 binding (p<0.0001, R 2 =0.66). I. Genomic heatmaps of ATAC-seq data, SMARCB1 and BRD9 CUT & RUN, and SMARCA4 ChIP-seq at the sites from (H) that are bound by SMARCB1 and BRD9 that show SMARCB1-dependent changes in ATAC accessibility, centered on the differentially accessible nucleosome-free regions. Sites are sorted by difference in the ATAC-seq nucleosome-free signal measured between SMARCB1 (SB1)- and GFP-induced G401 cells. The red sidebar indicates ATAC-up sites. The blue sidebar indicates ATAC-down sites.
    H3k27ac, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/h3k27ac/product/Cell Signaling Technology Inc
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    h3k27ac - by Bioz Stars, 2023-02
    95/100 stars
      Buy from Supplier

    Image Search Results


    p40 supplementation in early life stimulates short-term up-regulation of Setd1b gene expression, but sustained increase in epigenetic marks in mice. The treatment plans for detecting the short-term ( <xref ref-type=Figure 3 A ) and long-term effects ( Figure 3 B ) are described. ( A and B ) RNA was isolated from colonic tissues for RT-PCR analysis of Setd1b gene expression. Each symbol represents one mouse in A and B . ( C ) Paraffin-embedded tissue sections were prepared for immunohistochemistry using anti-H3K4me1 antibody and fluorescein isothiocyanate–conjugated secondary antibody (green), an epithelial cell marker using anti–E-cadherin antibody and Cy3-conjugated secondary antibody (red), and nuclei using 4′,6-diamidino-2-phenylindole (DAPI) staining (blue). Images were taken using a fluorescent microscope at 40×. ( D ) The numbers of H3K4me1 and E-cadherin double-positive cells per crypt are shown. N = 5 in each group. " width="100%" height="100%">

    Journal: Cellular and Molecular Gastroenterology and Hepatology

    Article Title: Exposure to p40 in Early Life Prevents Intestinal Inflammation in Adulthood Through Inducing a Long-Lasting Epigenetic Imprint on TGFβ

    doi: 10.1016/j.jcmgh.2021.01.004

    Figure Lengend Snippet: p40 supplementation in early life stimulates short-term up-regulation of Setd1b gene expression, but sustained increase in epigenetic marks in mice. The treatment plans for detecting the short-term ( Figure 3 A ) and long-term effects ( Figure 3 B ) are described. ( A and B ) RNA was isolated from colonic tissues for RT-PCR analysis of Setd1b gene expression. Each symbol represents one mouse in A and B . ( C ) Paraffin-embedded tissue sections were prepared for immunohistochemistry using anti-H3K4me1 antibody and fluorescein isothiocyanate–conjugated secondary antibody (green), an epithelial cell marker using anti–E-cadherin antibody and Cy3-conjugated secondary antibody (red), and nuclei using 4′,6-diamidino-2-phenylindole (DAPI) staining (blue). Images were taken using a fluorescent microscope at 40×. ( D ) The numbers of H3K4me1 and E-cadherin double-positive cells per crypt are shown. N = 5 in each group.

    Article Snippet: H3K4me1 and E-cadherin double staining was performed by incubating slides with a rabbit polyclonal anti-H3K4me1 antibody (5326; Cell Signaling) overnight followed by a mouse monoclonal anti–E-cadherin antibody (610181; BD Biosciences) for 1 hour at 4°C.

    Techniques: Expressing, Isolation, Reverse Transcription Polymerase Chain Reaction, Immunohistochemistry, Marker, Staining, Microscopy

    H2A.Z forms a complex with KDM1A, H3K4me1 and H3K4me2. A Western blot analysis revealed that H2A.Z is mainly expressed in the nucleus in HuccT-1 and RBE cells. B Immunofluorescence (IF) analysis of the nuclear localization of H2A.Z in HuccT-1 and RBE cells (400 × magnification). C Western blot analysis revealed that H2A.Z is mainly expressed in the nucleus in HuccT-1 and RBE cells with H2A.Z silencing. E Endogenous KDM1A, H3K4me1 and H3K4me2 were precipitated with the anti-H2A.Z antibody in HuccT-1, RBE and HIBEpic cells. F Western blot analysis revealed that KDM1A silencing can increase the relative level of SFRP1 expression

    Journal: BMC Cancer

    Article Title: The H2A.Z-KDM1A complex promotes tumorigenesis by localizing in the nucleus to promote SFRP1 promoter methylation in cholangiocarcinoma cells

    doi: 10.1186/s12885-022-10279-y

    Figure Lengend Snippet: H2A.Z forms a complex with KDM1A, H3K4me1 and H3K4me2. A Western blot analysis revealed that H2A.Z is mainly expressed in the nucleus in HuccT-1 and RBE cells. B Immunofluorescence (IF) analysis of the nuclear localization of H2A.Z in HuccT-1 and RBE cells (400 × magnification). C Western blot analysis revealed that H2A.Z is mainly expressed in the nucleus in HuccT-1 and RBE cells with H2A.Z silencing. E Endogenous KDM1A, H3K4me1 and H3K4me2 were precipitated with the anti-H2A.Z antibody in HuccT-1, RBE and HIBEpic cells. F Western blot analysis revealed that KDM1A silencing can increase the relative level of SFRP1 expression

    Article Snippet: Antibodies, including rabbit anti-H2A.Z (CST, Leiden, the Netherlands, 50722S), anti-H3K4me1 (CST, 5326S), rabbit polyclonal anti-Histone 3 (Proteintech, Chicago, USA, 17,168–1-AP), anti-H3K4me2 (CST, 9725S), anti-KDM1A (CST, 2139S), anti-SFRP1 (CST, 3534S), goat polyclonal anti-HP1α (Abcam, MA, USA, ab77256), mouse monoclonal anti-GST (Proteintech, 66,001–1-Ig), mouse monoclonal anti-GAPDH (Boster, Wuhan, China, BM1623) and IgG from healthy animals (Beyotime, Shanghai, China, A7007) were obtained from different companies.

    Techniques: Western Blot, Immunofluorescence, Expressing

    H2A.Z binds to the upstream region of the SFRP1 promoter and reduces SFRP1 expression. A Graphical representation of the CpG sites in the SFRP1 promoter. B ChIP assay of KDM1A, H3K4me1 and H3K4me2 enrichment in the P3 region upstream of the SFRP1 promoter. IgG was used as the negative control. Relative fold enrichment = [%(ChIP/Input)]/[%(IgG/Input)]. C BSP analysis of the CpG site methylation rate. Each dot represents one CpG site. White represents the absence of methylation, and pale green to deep yellow represent increasing methylation rates. D Quantitative RT–PCR analysis of the SFRP1 mRNA transcript level relative to the GAPDH mRNA transcript level in the blank control, LV-shRNA-NC, LV-shR-H2A.Z and LV-NC-H2A.Z + 5-aza-dC groups. The data are expressed as the individual mean values or the mean ± SD of each group in three independent experiments. ** p < 0.01, *** p < 0.001

    Journal: BMC Cancer

    Article Title: The H2A.Z-KDM1A complex promotes tumorigenesis by localizing in the nucleus to promote SFRP1 promoter methylation in cholangiocarcinoma cells

    doi: 10.1186/s12885-022-10279-y

    Figure Lengend Snippet: H2A.Z binds to the upstream region of the SFRP1 promoter and reduces SFRP1 expression. A Graphical representation of the CpG sites in the SFRP1 promoter. B ChIP assay of KDM1A, H3K4me1 and H3K4me2 enrichment in the P3 region upstream of the SFRP1 promoter. IgG was used as the negative control. Relative fold enrichment = [%(ChIP/Input)]/[%(IgG/Input)]. C BSP analysis of the CpG site methylation rate. Each dot represents one CpG site. White represents the absence of methylation, and pale green to deep yellow represent increasing methylation rates. D Quantitative RT–PCR analysis of the SFRP1 mRNA transcript level relative to the GAPDH mRNA transcript level in the blank control, LV-shRNA-NC, LV-shR-H2A.Z and LV-NC-H2A.Z + 5-aza-dC groups. The data are expressed as the individual mean values or the mean ± SD of each group in three independent experiments. ** p < 0.01, *** p < 0.001

    Article Snippet: Antibodies, including rabbit anti-H2A.Z (CST, Leiden, the Netherlands, 50722S), anti-H3K4me1 (CST, 5326S), rabbit polyclonal anti-Histone 3 (Proteintech, Chicago, USA, 17,168–1-AP), anti-H3K4me2 (CST, 9725S), anti-KDM1A (CST, 2139S), anti-SFRP1 (CST, 3534S), goat polyclonal anti-HP1α (Abcam, MA, USA, ab77256), mouse monoclonal anti-GST (Proteintech, 66,001–1-Ig), mouse monoclonal anti-GAPDH (Boster, Wuhan, China, BM1623) and IgG from healthy animals (Beyotime, Shanghai, China, A7007) were obtained from different companies.

    Techniques: Expressing, Negative Control, Methylation, Quantitative RT-PCR, shRNA

    Schematic illustration of the role of H2A.Z in regulating SFRP1 promoter activity in ICC. In the nucleus, H2A.Z recruits KDM1A, H3K4me1 and H3K4me2 to form a complex to promote demethylation upstream of the SFRP1 promoter and coordinates with HP1α, which is located at downstream CpG islands and recruits SUV39H1/H3K9me3/DNMTs to repress SFRP1 transcription

    Journal: BMC Cancer

    Article Title: The H2A.Z-KDM1A complex promotes tumorigenesis by localizing in the nucleus to promote SFRP1 promoter methylation in cholangiocarcinoma cells

    doi: 10.1186/s12885-022-10279-y

    Figure Lengend Snippet: Schematic illustration of the role of H2A.Z in regulating SFRP1 promoter activity in ICC. In the nucleus, H2A.Z recruits KDM1A, H3K4me1 and H3K4me2 to form a complex to promote demethylation upstream of the SFRP1 promoter and coordinates with HP1α, which is located at downstream CpG islands and recruits SUV39H1/H3K9me3/DNMTs to repress SFRP1 transcription

    Article Snippet: Antibodies, including rabbit anti-H2A.Z (CST, Leiden, the Netherlands, 50722S), anti-H3K4me1 (CST, 5326S), rabbit polyclonal anti-Histone 3 (Proteintech, Chicago, USA, 17,168–1-AP), anti-H3K4me2 (CST, 9725S), anti-KDM1A (CST, 2139S), anti-SFRP1 (CST, 3534S), goat polyclonal anti-HP1α (Abcam, MA, USA, ab77256), mouse monoclonal anti-GST (Proteintech, 66,001–1-Ig), mouse monoclonal anti-GAPDH (Boster, Wuhan, China, BM1623) and IgG from healthy animals (Beyotime, Shanghai, China, A7007) were obtained from different companies.

    Techniques: Activity Assay

    A. SMARCB1 CUT & RUN following expression of SMARCB1 in G401 RT cells for 24 h identifies 94,114 SMARCB1 peaks. Genomic binding signal from SMARCB1- and GFP-induced G401 (SB1, GFP) cells is sorted by SMARCB1 enrichment and clustered by genomic elements defined by chromatin marks generated from MNase-ChIP. Traditional enhancers (TEs, black) and super enhancers (SEs, gold) were called by using H3K27Ac data from SB1 cells according to Rank Ordering of Super Enhancers (ROSE). Promoter-associated peaks outside a ROSE-defined enhancer (Ps, green) were called within 1 kb of an H3K4me3-enriched promoter. Primed enhancer sites (PEs, dark blue) are H3K4me1-enriched, H3K27Ac-negative regions >1 kb from the nearest TSS. Data shown are the average of two biological replicates. B-G. BRD9, SMARCA4, and SMARCB1 genomic binding data from 15,471 differentially bound BRD9 CUT & RUN peaks (SB1 vs. GFP, FDR < 0.05). BRD9 CUT & RUN data are the average of 3 biological replicates. B-D BRD9, SMARCA4, and SMARCB1 genomic binding data from 13,410 sites with significant increase in BRD9 upon SMARCB1 expression (SB1 vs. GFP, FDR < 0.05) (B). Sites gaining BRD9 are annotated with ROSE and histone modification data analysis from SMARCB1-induced G401 cells (C). Circle graphs show the percentage of BRD9-up sites bound by SMARCB1 (D). E-G. BRD9, SMARCA4, and SMARCB1 genomic binding data from 2,061 sites with a significant decrease in BRD9 (SB1 vs. GFP, FDR < 0.05) (E). Sites losing BRD9 are annotated with ROSE and histone modification data analysis from GFP-induced (negative control) G401 cells (F). Sites >1 kb from a TSS with no H3K4me1 were classified as TSS-distal sites (TDs). A black box indicates a region within TEs, SEs, and Ps where SMARCA4 is also lost upon SMARCB1 rescue (E, F). Circle graphs show the percentage of BRD9-down sites bound by SMARCB1 (G). H. Linear regression comparing SMARCB1-dependent changes in accessibility to fold-change BRD9 enrichment between SMARCB1 (SB1)- and GFP-induced G401 cells at sites where SMARCB1 and BRD9 were detected in at least one sample at a differentially accessible region (SMARCB1 + /BRD9 + Differentially Accessible Regions). SMARCB1 + /BRD9 + differentially accessible regions are correlated with SMARCB1-dependent changes in BRD9 binding (p<0.0001, R 2 =0.66). I. Genomic heatmaps of ATAC-seq data, SMARCB1 and BRD9 CUT & RUN, and SMARCA4 ChIP-seq at the sites from (H) that are bound by SMARCB1 and BRD9 that show SMARCB1-dependent changes in ATAC accessibility, centered on the differentially accessible nucleosome-free regions. Sites are sorted by difference in the ATAC-seq nucleosome-free signal measured between SMARCB1 (SB1)- and GFP-induced G401 cells. The red sidebar indicates ATAC-up sites. The blue sidebar indicates ATAC-down sites.

    Journal: bioRxiv

    Article Title: Functional interplay between SWI/SNF complexes underlies BRD9 dependency in SMARCB1-mutant cancers

    doi: 10.1101/2022.08.07.503080

    Figure Lengend Snippet: A. SMARCB1 CUT & RUN following expression of SMARCB1 in G401 RT cells for 24 h identifies 94,114 SMARCB1 peaks. Genomic binding signal from SMARCB1- and GFP-induced G401 (SB1, GFP) cells is sorted by SMARCB1 enrichment and clustered by genomic elements defined by chromatin marks generated from MNase-ChIP. Traditional enhancers (TEs, black) and super enhancers (SEs, gold) were called by using H3K27Ac data from SB1 cells according to Rank Ordering of Super Enhancers (ROSE). Promoter-associated peaks outside a ROSE-defined enhancer (Ps, green) were called within 1 kb of an H3K4me3-enriched promoter. Primed enhancer sites (PEs, dark blue) are H3K4me1-enriched, H3K27Ac-negative regions >1 kb from the nearest TSS. Data shown are the average of two biological replicates. B-G. BRD9, SMARCA4, and SMARCB1 genomic binding data from 15,471 differentially bound BRD9 CUT & RUN peaks (SB1 vs. GFP, FDR < 0.05). BRD9 CUT & RUN data are the average of 3 biological replicates. B-D BRD9, SMARCA4, and SMARCB1 genomic binding data from 13,410 sites with significant increase in BRD9 upon SMARCB1 expression (SB1 vs. GFP, FDR < 0.05) (B). Sites gaining BRD9 are annotated with ROSE and histone modification data analysis from SMARCB1-induced G401 cells (C). Circle graphs show the percentage of BRD9-up sites bound by SMARCB1 (D). E-G. BRD9, SMARCA4, and SMARCB1 genomic binding data from 2,061 sites with a significant decrease in BRD9 (SB1 vs. GFP, FDR < 0.05) (E). Sites losing BRD9 are annotated with ROSE and histone modification data analysis from GFP-induced (negative control) G401 cells (F). Sites >1 kb from a TSS with no H3K4me1 were classified as TSS-distal sites (TDs). A black box indicates a region within TEs, SEs, and Ps where SMARCA4 is also lost upon SMARCB1 rescue (E, F). Circle graphs show the percentage of BRD9-down sites bound by SMARCB1 (G). H. Linear regression comparing SMARCB1-dependent changes in accessibility to fold-change BRD9 enrichment between SMARCB1 (SB1)- and GFP-induced G401 cells at sites where SMARCB1 and BRD9 were detected in at least one sample at a differentially accessible region (SMARCB1 + /BRD9 + Differentially Accessible Regions). SMARCB1 + /BRD9 + differentially accessible regions are correlated with SMARCB1-dependent changes in BRD9 binding (p<0.0001, R 2 =0.66). I. Genomic heatmaps of ATAC-seq data, SMARCB1 and BRD9 CUT & RUN, and SMARCA4 ChIP-seq at the sites from (H) that are bound by SMARCB1 and BRD9 that show SMARCB1-dependent changes in ATAC accessibility, centered on the differentially accessible nucleosome-free regions. Sites are sorted by difference in the ATAC-seq nucleosome-free signal measured between SMARCB1 (SB1)- and GFP-induced G401 cells. The red sidebar indicates ATAC-up sites. The blue sidebar indicates ATAC-down sites.

    Article Snippet: Histone modification ChIPs were performed by using 10 µg of chromatin each incubated with the recommended amount of H3K27Ac (Cell Signaling #8173, 5ul), H3K4me1 (Cell Signaling #5326, 10 µL), and H3K4me3 (Cell Signaling #9751, 10 µL), respectively.

    Techniques: Expressing, Binding Assay, Generated, Modification, Negative Control, ChIP-sequencing