anti-h3k4me3 antibodies Search Results


  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 97
    Millipore anti h3k4me3 antibody
    Status of histone modifications and pol II binding in the proximal regions of STAT6 target TSSs. (A) Distribution of the averaged ChIP Seq tags for <t>H3K4me3</t> (top panels), H3Ac (middle panels) and pol II (bottom panels) in Ramos cells. Data from active target genes (STAT6 binding plus TSS induction in Ramos cells) are shown in the left panels, and data from silent target genes (STAT6 binding plus TSS induction in BEAS2B cells but both negative in Ramos cells) are shown in the right panels. Blue, green, red and purple lines indicate the results for the IP (IL-4 (+)), IP (IL-4 (−)), WCE (IL-4 (+)) and WCE (IL-4 (−)) experiments, respectively. On the x -axis, the position of the associated TSS is designated as zero. (B) Results of an analysis similar to that shown in (A) in BEAS2B cells.
    Anti H3k4me3 Antibody, supplied by Millipore, used in various techniques. Bioz Stars score: 97/100, based on 447 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/anti h3k4me3 antibody/product/Millipore
    Average 97 stars, based on 447 article reviews
    Price from $9.99 to $1999.99
    anti h3k4me3 antibody - by Bioz Stars, 2020-08
    97/100 stars
      Buy from Supplier

    91
    Abcam anti h3k4me3 antibody
    IL-6 promotes NEAT1 transcription through STAT3 and <t>H3K4me3.</t> (A) NEAT1_2 promoter methylation in the QGY-7703 cells following IL-6 stimulation as indicated time. The black arrow shows the unmethylated bands. M, methylated; U, unmethylated. IL-6 6h, cells were treated with IL-6 for 6 h. IL-6 10h, cells were treated with IL-6 for 10 h. (B) H3K4me3, H3K9me3, H3K27me3 or H4K20me3 modifications at the NEAT1 promoter in the QGY-7703 cells with or without IL-6 stimulation were detected by ChIP assay. 0-1k: the sequence of 0 to 1000bp upstream transcription start site (TSS). 1k-2k: the sequence of 1000 to 2000bp upstream TSS (* p
    Anti H3k4me3 Antibody, supplied by Abcam, used in various techniques. Bioz Stars score: 91/100, based on 181 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/anti h3k4me3 antibody/product/Abcam
    Average 91 stars, based on 181 article reviews
    Price from $9.99 to $1999.99
    anti h3k4me3 antibody - by Bioz Stars, 2020-08
    91/100 stars
      Buy from Supplier

    91
    Cell Signaling Technology Inc anti h3k4me3 antibody
    DPY30 expression promotes EMT in SKOV3 cells in vitro . DPY30 methylates <t>H3K4me3</t> at the vimentin promoter. (A) sh-DPY30 expression enhanced the expression of the EMT marker E-cadherin and attenuated the expression of the EMT markers N-cadherin, vimentin and Snail in SKOV3 cells. (B) According to the western blotting results, H3K4me3 expression was increased in SKOV3 cells expressing sh-DPY30 compared with those expressing sh-Control. Total histone H3 served as a loading control. (C) Upon chromatin immunoprecipitation, the level of H3K4me3 at the vimentin promoter was lower in cells expressing sh-DPY30 than in control cells. * P
    Anti H3k4me3 Antibody, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 91/100, based on 31 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/anti h3k4me3 antibody/product/Cell Signaling Technology Inc
    Average 91 stars, based on 31 article reviews
    Price from $9.99 to $1999.99
    anti h3k4me3 antibody - by Bioz Stars, 2020-08
    91/100 stars
      Buy from Supplier

    88
    Upstate Biotechnology Inc anti h3k4me3 antibodies
    DPY30 expression promotes EMT in SKOV3 cells in vitro . DPY30 methylates <t>H3K4me3</t> at the vimentin promoter. (A) sh-DPY30 expression enhanced the expression of the EMT marker E-cadherin and attenuated the expression of the EMT markers N-cadherin, vimentin and Snail in SKOV3 cells. (B) According to the western blotting results, H3K4me3 expression was increased in SKOV3 cells expressing sh-DPY30 compared with those expressing sh-Control. Total histone H3 served as a loading control. (C) Upon chromatin immunoprecipitation, the level of H3K4me3 at the vimentin promoter was lower in cells expressing sh-DPY30 than in control cells. * P
    Anti H3k4me3 Antibodies, supplied by Upstate Biotechnology Inc, used in various techniques. Bioz Stars score: 88/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/anti h3k4me3 antibodies/product/Upstate Biotechnology Inc
    Average 88 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    anti h3k4me3 antibodies - by Bioz Stars, 2020-08
    88/100 stars
      Buy from Supplier

    99
    Active Motif anti h3k4me3
    Interaction between RBFox2 and PRC2 (A) Co-IP of RBFox2 with key components of PRC1 and PRC2 in MEFs. (B) Reciprocal co-IP of RBFox2 with PRC2 in a RNA-independent manner. Before immunoprecipitation, whole-cell extracts were treated with either RNase A (R) or benzonase (B) for 30 min at room temperature. GAPDH served as negative control for immunoprecipitation. (C) Re-ChIP confirms co-binding of SUZ12 and RBFox2 on the TSS regions of two bivalent genes ( Egr2 and Arxes4 ), but not on Slc6a12 without <t>H3K4me3</t> or H3K27me3 signals. ChIP signals are presented as percentage of input. Data are compared to immunoglobulin G control and are presented as mean ± SEM. **p
    Anti H3k4me3, supplied by Active Motif, used in various techniques. Bioz Stars score: 99/100, based on 755 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/anti h3k4me3/product/Active Motif
    Average 99 stars, based on 755 article reviews
    Price from $9.99 to $1999.99
    anti h3k4me3 - by Bioz Stars, 2020-08
    99/100 stars
      Buy from Supplier

    88
    Diagenode anti h3k4me3 polyclonal antibody
    Interaction between RBFox2 and PRC2 (A) Co-IP of RBFox2 with key components of PRC1 and PRC2 in MEFs. (B) Reciprocal co-IP of RBFox2 with PRC2 in a RNA-independent manner. Before immunoprecipitation, whole-cell extracts were treated with either RNase A (R) or benzonase (B) for 30 min at room temperature. GAPDH served as negative control for immunoprecipitation. (C) Re-ChIP confirms co-binding of SUZ12 and RBFox2 on the TSS regions of two bivalent genes ( Egr2 and Arxes4 ), but not on Slc6a12 without <t>H3K4me3</t> or H3K27me3 signals. ChIP signals are presented as percentage of input. Data are compared to immunoglobulin G control and are presented as mean ± SEM. **p
    Anti H3k4me3 Polyclonal Antibody, supplied by Diagenode, used in various techniques. Bioz Stars score: 88/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/anti h3k4me3 polyclonal antibody/product/Diagenode
    Average 88 stars, based on 4 article reviews
    Price from $9.99 to $1999.99
    anti h3k4me3 polyclonal antibody - by Bioz Stars, 2020-08
    88/100 stars
      Buy from Supplier

    Image Search Results


    Status of histone modifications and pol II binding in the proximal regions of STAT6 target TSSs. (A) Distribution of the averaged ChIP Seq tags for H3K4me3 (top panels), H3Ac (middle panels) and pol II (bottom panels) in Ramos cells. Data from active target genes (STAT6 binding plus TSS induction in Ramos cells) are shown in the left panels, and data from silent target genes (STAT6 binding plus TSS induction in BEAS2B cells but both negative in Ramos cells) are shown in the right panels. Blue, green, red and purple lines indicate the results for the IP (IL-4 (+)), IP (IL-4 (−)), WCE (IL-4 (+)) and WCE (IL-4 (−)) experiments, respectively. On the x -axis, the position of the associated TSS is designated as zero. (B) Results of an analysis similar to that shown in (A) in BEAS2B cells.

    Journal: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

    Article Title: Characterization of STAT6 Target Genes in Human B Cells and Lung Epithelial Cells

    doi: 10.1093/dnares/dsr025

    Figure Lengend Snippet: Status of histone modifications and pol II binding in the proximal regions of STAT6 target TSSs. (A) Distribution of the averaged ChIP Seq tags for H3K4me3 (top panels), H3Ac (middle panels) and pol II (bottom panels) in Ramos cells. Data from active target genes (STAT6 binding plus TSS induction in Ramos cells) are shown in the left panels, and data from silent target genes (STAT6 binding plus TSS induction in BEAS2B cells but both negative in Ramos cells) are shown in the right panels. Blue, green, red and purple lines indicate the results for the IP (IL-4 (+)), IP (IL-4 (−)), WCE (IL-4 (+)) and WCE (IL-4 (−)) experiments, respectively. On the x -axis, the position of the associated TSS is designated as zero. (B) Results of an analysis similar to that shown in (A) in BEAS2B cells.

    Article Snippet: Anti-STAT-6 antibody (Santa Cruz, M-20), anti-RNA pol II antibody (Abcam, ab817), anti-H3K4me3 antibody (ab1012) and anti-H3Ac antibody (Millipore, 06–599) were used for the indicated experiments.

    Techniques: Binding Assay, Chromatin Immunoprecipitation

    DLL4-enriched permissive histone mark H3K4me3 around Foxp3 promoter and consensus non-coding sequences during iTreg differentiation. a 2 × 10 6 of naive CD4 T cells were skewed toward Th0 or iT reg differentiation with or without DLL4 stimulation in vitro. Chromatin immunoprecipitation were performed to detect H3K4me3 around Foxp3 promoter, consensus non-coding sequence (CNS)1, CNS2, CNS3 after 72 h. b Changes of H3K4me and H3K4me3 by DLL4 stimulation during iT reg differentiation was detected at 48 h of skewing. c H3K4me3 kinetics at Foxp3 CNS1 after 6 h, 24 h, 48 h and 72 h post iT reg differentiation were measured with or without DLL4 stimulation in vitro. Data represent mean ± SEM. Data were from one experiment representative of two to three experiments. * P

    Journal: Mucosal immunology

    Article Title: Notch ligand Delta-like 4 induces epigenetic regulation of Treg cell differentiation and function in viral infection

    doi: 10.1038/s41385-018-0052-1

    Figure Lengend Snippet: DLL4-enriched permissive histone mark H3K4me3 around Foxp3 promoter and consensus non-coding sequences during iTreg differentiation. a 2 × 10 6 of naive CD4 T cells were skewed toward Th0 or iT reg differentiation with or without DLL4 stimulation in vitro. Chromatin immunoprecipitation were performed to detect H3K4me3 around Foxp3 promoter, consensus non-coding sequence (CNS)1, CNS2, CNS3 after 72 h. b Changes of H3K4me and H3K4me3 by DLL4 stimulation during iT reg differentiation was detected at 48 h of skewing. c H3K4me3 kinetics at Foxp3 CNS1 after 6 h, 24 h, 48 h and 72 h post iT reg differentiation were measured with or without DLL4 stimulation in vitro. Data represent mean ± SEM. Data were from one experiment representative of two to three experiments. * P

    Article Snippet: After three washes, sample were labeled with primary antibody anti-H3K4me3 (Millipore #07-473) in 1:200 dilution for 30 min at room temperature and secondary antibody antigen presenting cell (APC) or fluorescein isothiocyanate-antirabbit antibody for 20 min at room temperature.

    Techniques: In Vitro, Chromatin Immunoprecipitation, Sequencing

    Smyd3 regulated DLL4-enhanced iT reg differentiation and function in vitro. a Naive CD4 T cells (10 6 ) from wild-type B6 spleen were activated (Th0) or differentiated to Th1, Th2, Th17, Th9, iT reg , and IL-27 T R 1. After 72 h, SMYD3 were blotted. b Naive CD4 T cells (10 6 ) from Cre− control or Cre + CD4-specific SMYD3 conditional knockout (cKO) were differentiated to iT reg . After 72 h, SMYD3 level were quantified by western blotting. c Smyd3 mRNA level were measure in iT reg and DLL4-stimulated iT reg differentiation at 24, 48, and 72 h from Cre− control and Cre + Smyd3 cKO. d Naive CD4 T cells (2 × 10 6 ) from Cre− control with or without DLL4 stimulation or Cre + CD4-specific SMYD3 were differentiated to iT reg . After 72 h, H3K4me3 were precipitated, and Foxp3 promoter and CNS1, 2, 3 were qPCR quantified compared with input control. e Naive CD4 T cells (10 6 ) from Cre− control or Cre + SMYD3 cKO were activated (Th0) or differentiated to iT reg with or without DLL4. After 72 h of differentiation, Foxp3 and CD25 were labeled and quantified by flow cytometry. f Naive CD4 T cells (10 6 ) from Cre− control or Cre + SMYD3 cKO were activated (Th0) or differentiated to iT reg with or without DLL4. After 72 h of differentiation, both Th0 and iT reg were rested in IL-2 10 ng/mL for another 72 h. Foxp3 were detected and quantified by flow cytometry. g After 6 days of iT reg differentiation with DLL4 as described in f , viable DLL4-exposed iT reg were sorted out as DAPI − CD25+ and co-cultured with Cell Trace violet (CTV) labeled CD45.1+ naive T cells with anti-CD3/anti-CD28 beads. After 3 days in co-culture, proliferation was assessed by CTV dilution in CD45.1 + responder cells. Data represent mean ± SEM. Data were from one experiment representative of two to three experiments. * P

    Journal: Mucosal immunology

    Article Title: Notch ligand Delta-like 4 induces epigenetic regulation of Treg cell differentiation and function in viral infection

    doi: 10.1038/s41385-018-0052-1

    Figure Lengend Snippet: Smyd3 regulated DLL4-enhanced iT reg differentiation and function in vitro. a Naive CD4 T cells (10 6 ) from wild-type B6 spleen were activated (Th0) or differentiated to Th1, Th2, Th17, Th9, iT reg , and IL-27 T R 1. After 72 h, SMYD3 were blotted. b Naive CD4 T cells (10 6 ) from Cre− control or Cre + CD4-specific SMYD3 conditional knockout (cKO) were differentiated to iT reg . After 72 h, SMYD3 level were quantified by western blotting. c Smyd3 mRNA level were measure in iT reg and DLL4-stimulated iT reg differentiation at 24, 48, and 72 h from Cre− control and Cre + Smyd3 cKO. d Naive CD4 T cells (2 × 10 6 ) from Cre− control with or without DLL4 stimulation or Cre + CD4-specific SMYD3 were differentiated to iT reg . After 72 h, H3K4me3 were precipitated, and Foxp3 promoter and CNS1, 2, 3 were qPCR quantified compared with input control. e Naive CD4 T cells (10 6 ) from Cre− control or Cre + SMYD3 cKO were activated (Th0) or differentiated to iT reg with or without DLL4. After 72 h of differentiation, Foxp3 and CD25 were labeled and quantified by flow cytometry. f Naive CD4 T cells (10 6 ) from Cre− control or Cre + SMYD3 cKO were activated (Th0) or differentiated to iT reg with or without DLL4. After 72 h of differentiation, both Th0 and iT reg were rested in IL-2 10 ng/mL for another 72 h. Foxp3 were detected and quantified by flow cytometry. g After 6 days of iT reg differentiation with DLL4 as described in f , viable DLL4-exposed iT reg were sorted out as DAPI − CD25+ and co-cultured with Cell Trace violet (CTV) labeled CD45.1+ naive T cells with anti-CD3/anti-CD28 beads. After 3 days in co-culture, proliferation was assessed by CTV dilution in CD45.1 + responder cells. Data represent mean ± SEM. Data were from one experiment representative of two to three experiments. * P

    Article Snippet: After three washes, sample were labeled with primary antibody anti-H3K4me3 (Millipore #07-473) in 1:200 dilution for 30 min at room temperature and secondary antibody antigen presenting cell (APC) or fluorescein isothiocyanate-antirabbit antibody for 20 min at room temperature.

    Techniques: In Vitro, Knock-Out, Western Blot, Real-time Polymerase Chain Reaction, Labeling, Flow Cytometry, Cytometry, Cell Culture, Co-Culture Assay

    Levels of Vκ gene germline transcription and H3K4me3 modification in pre-B cells. A, Real-time PCR assays were used to measure Igκ gene germline transcripts arising from the 5′ promoter (5′GL) and from the indicated Vκ

    Journal: Journal of immunology (Baltimore, Md. : 1950)

    Article Title: V? gene repertoire and locus contraction are specified by critical DNase I hypersensitive sites within the V?-J? intervening region

    doi: 10.4049/jimmunol.1203127

    Figure Lengend Snippet: Levels of Vκ gene germline transcription and H3K4me3 modification in pre-B cells. A, Real-time PCR assays were used to measure Igκ gene germline transcripts arising from the 5′ promoter (5′GL) and from the indicated Vκ

    Article Snippet: Rabbit anti-CTCF antibodies (Millipore, 07-729), and Rabbit anti-H3K4me3 antibodies (Millipore, 07-473) were used for ChIP.

    Techniques: Modification, Real-time Polymerase Chain Reaction

    Activation of PfAP2-G A) Only a small fraction (1-6%) of asexually growing subclone 9A schizonts (see Fig. S7 for details) express detectable levels of PfAP2-G-HAx3 (first row). H3K4me3 staining was performed in parallel to confirm full permeabilization (second row), scale bar = 10μm. Representative of n=3. B) The percentage of PfAP2-G-HAx3 positive cells is highly predictive (R 2 = 0.94) of subsequent gametocyte formation levels. C) Model of PfAP2-G activation and function.

    Journal: Nature

    Article Title: A transcriptional switch underlies commitment to sexual development in human malaria parasites

    doi: 10.1038/nature12920

    Figure Lengend Snippet: Activation of PfAP2-G A) Only a small fraction (1-6%) of asexually growing subclone 9A schizonts (see Fig. S7 for details) express detectable levels of PfAP2-G-HAx3 (first row). H3K4me3 staining was performed in parallel to confirm full permeabilization (second row), scale bar = 10μm. Representative of n=3. B) The percentage of PfAP2-G-HAx3 positive cells is highly predictive (R 2 = 0.94) of subsequent gametocyte formation levels. C) Model of PfAP2-G activation and function.

    Article Snippet: Smears were incubated with rabbit anti-HA (1:100; Life technologies 71-5500) or rabbit anti-H3K4me3 (1:10,000; Millipore 05-745) antibodies.

    Techniques: Activation Assay, Staining

    IL-6 promotes NEAT1 transcription through STAT3 and H3K4me3. (A) NEAT1_2 promoter methylation in the QGY-7703 cells following IL-6 stimulation as indicated time. The black arrow shows the unmethylated bands. M, methylated; U, unmethylated. IL-6 6h, cells were treated with IL-6 for 6 h. IL-6 10h, cells were treated with IL-6 for 10 h. (B) H3K4me3, H3K9me3, H3K27me3 or H4K20me3 modifications at the NEAT1 promoter in the QGY-7703 cells with or without IL-6 stimulation were detected by ChIP assay. 0-1k: the sequence of 0 to 1000bp upstream transcription start site (TSS). 1k-2k: the sequence of 1000 to 2000bp upstream TSS (* p

    Journal: Oncoimmunology

    Article Title: NEAT1 paraspeckle promotes human hepatocellular carcinoma progression by strengthening IL-6/STAT3 signaling

    doi: 10.1080/2162402X.2018.1503913

    Figure Lengend Snippet: IL-6 promotes NEAT1 transcription through STAT3 and H3K4me3. (A) NEAT1_2 promoter methylation in the QGY-7703 cells following IL-6 stimulation as indicated time. The black arrow shows the unmethylated bands. M, methylated; U, unmethylated. IL-6 6h, cells were treated with IL-6 for 6 h. IL-6 10h, cells were treated with IL-6 for 10 h. (B) H3K4me3, H3K9me3, H3K27me3 or H4K20me3 modifications at the NEAT1 promoter in the QGY-7703 cells with or without IL-6 stimulation were detected by ChIP assay. 0-1k: the sequence of 0 to 1000bp upstream transcription start site (TSS). 1k-2k: the sequence of 1000 to 2000bp upstream TSS (* p

    Article Snippet: Then 3μg anti-H3K4me3 antibody (Abcam, USA), anti-H3K9me3 antibody (Abcam, USA), anti-H3K27me3 antibody (Abcam, USA), anti-H4K20me3 antibody (Abcam, USA), or IgG was added to each nuclear extract, and incubated at 4°C overnight.

    Techniques: Methylation, Chromatin Immunoprecipitation, Sequencing

    DPY30 expression promotes EMT in SKOV3 cells in vitro . DPY30 methylates H3K4me3 at the vimentin promoter. (A) sh-DPY30 expression enhanced the expression of the EMT marker E-cadherin and attenuated the expression of the EMT markers N-cadherin, vimentin and Snail in SKOV3 cells. (B) According to the western blotting results, H3K4me3 expression was increased in SKOV3 cells expressing sh-DPY30 compared with those expressing sh-Control. Total histone H3 served as a loading control. (C) Upon chromatin immunoprecipitation, the level of H3K4me3 at the vimentin promoter was lower in cells expressing sh-DPY30 than in control cells. * P

    Journal: International Journal of Molecular Medicine

    Article Title: DPY30 is required for the enhanced proliferation, motility and epithelial-mesenchymal transition of epithelial ovarian cancer cells

    doi: 10.3892/ijmm.2018.3869

    Figure Lengend Snippet: DPY30 expression promotes EMT in SKOV3 cells in vitro . DPY30 methylates H3K4me3 at the vimentin promoter. (A) sh-DPY30 expression enhanced the expression of the EMT marker E-cadherin and attenuated the expression of the EMT markers N-cadherin, vimentin and Snail in SKOV3 cells. (B) According to the western blotting results, H3K4me3 expression was increased in SKOV3 cells expressing sh-DPY30 compared with those expressing sh-Control. Total histone H3 served as a loading control. (C) Upon chromatin immunoprecipitation, the level of H3K4me3 at the vimentin promoter was lower in cells expressing sh-DPY30 than in control cells. * P

    Article Snippet: Anti-H3K4me3 antibody (cat. no. 9751; 1:50) was obtained from Cell Signaling Technology, Inc., and anti-DPY30 antibody (cat. no. ab214010; 1:50) was obtained from Abcam.

    Techniques: Expressing, In Vitro, Marker, Western Blot, Chromatin Immunoprecipitation

    Interaction between RBFox2 and PRC2 (A) Co-IP of RBFox2 with key components of PRC1 and PRC2 in MEFs. (B) Reciprocal co-IP of RBFox2 with PRC2 in a RNA-independent manner. Before immunoprecipitation, whole-cell extracts were treated with either RNase A (R) or benzonase (B) for 30 min at room temperature. GAPDH served as negative control for immunoprecipitation. (C) Re-ChIP confirms co-binding of SUZ12 and RBFox2 on the TSS regions of two bivalent genes ( Egr2 and Arxes4 ), but not on Slc6a12 without H3K4me3 or H3K27me3 signals. ChIP signals are presented as percentage of input. Data are compared to immunoglobulin G control and are presented as mean ± SEM. **p

    Journal: Molecular cell

    Article Title: RBFox2 Binds Nascent RNA to Globally Regulate Polycomb Complex 2 Targeting in Mammalian Genomes

    doi: 10.1016/j.molcel.2016.04.013

    Figure Lengend Snippet: Interaction between RBFox2 and PRC2 (A) Co-IP of RBFox2 with key components of PRC1 and PRC2 in MEFs. (B) Reciprocal co-IP of RBFox2 with PRC2 in a RNA-independent manner. Before immunoprecipitation, whole-cell extracts were treated with either RNase A (R) or benzonase (B) for 30 min at room temperature. GAPDH served as negative control for immunoprecipitation. (C) Re-ChIP confirms co-binding of SUZ12 and RBFox2 on the TSS regions of two bivalent genes ( Egr2 and Arxes4 ), but not on Slc6a12 without H3K4me3 or H3K27me3 signals. ChIP signals are presented as percentage of input. Data are compared to immunoglobulin G control and are presented as mean ± SEM. **p

    Article Snippet: ChIP-seq was performed as described previously ( ) using anti-RBFox2 (Bethyl, A300-864A), anti-SUZ12 (Cell Signaling, D39F6), anti-H3K27me3 (Active Motif, 61017), anti-H3K4me3 (Active Motif, 39159) or anti-Pol II (Santa Cruz Biotechnology, sc-899).

    Techniques: Co-Immunoprecipitation Assay, Immunoprecipitation, Negative Control, Chromatin Immunoprecipitation, Binding Assay

    Functional Requirement for RBFox2 to Mediate Global PRC2 Targeting (A) ChIP-seq signals on a representative chromosomal segment for RBFox2, SUZ12, and H3K27me3 before and after siRNA-mediated RBFox2 knockdown (siR) in MEFs. The y axis indicates the read density per 10 million total reads (RP10M). (B–E) Sorted ChIP-seq signals for SUZ12, H3K27me3, RBFox2, and H3K4me3 at TSS regions in control siRNA-treated (B), SUZ12 siRNA-treated (C), RBFox2 siRNA-treated (D), and DRB-treated (E) MEFs. The data were sorted according to mean SUZ12 ChIP-seq signals in control siRNA-treated MEFs. All ChIP-seq data were normalized by total reads after subtracting input signals. The numbers beside the color bar indicate the read density per million. See also Figure S3 and Table S3. (F–H) Responses of the indicated ChIP-seq signals to RBFox2 knockdown on different gene classes (bivalent, H3K27me3 only, or H3K4me3 only) in MEFs. See also Figure S4 and Table S4 on related functional data from C2C12 cells.

    Journal: Molecular cell

    Article Title: RBFox2 Binds Nascent RNA to Globally Regulate Polycomb Complex 2 Targeting in Mammalian Genomes

    doi: 10.1016/j.molcel.2016.04.013

    Figure Lengend Snippet: Functional Requirement for RBFox2 to Mediate Global PRC2 Targeting (A) ChIP-seq signals on a representative chromosomal segment for RBFox2, SUZ12, and H3K27me3 before and after siRNA-mediated RBFox2 knockdown (siR) in MEFs. The y axis indicates the read density per 10 million total reads (RP10M). (B–E) Sorted ChIP-seq signals for SUZ12, H3K27me3, RBFox2, and H3K4me3 at TSS regions in control siRNA-treated (B), SUZ12 siRNA-treated (C), RBFox2 siRNA-treated (D), and DRB-treated (E) MEFs. The data were sorted according to mean SUZ12 ChIP-seq signals in control siRNA-treated MEFs. All ChIP-seq data were normalized by total reads after subtracting input signals. The numbers beside the color bar indicate the read density per million. See also Figure S3 and Table S3. (F–H) Responses of the indicated ChIP-seq signals to RBFox2 knockdown on different gene classes (bivalent, H3K27me3 only, or H3K4me3 only) in MEFs. See also Figure S4 and Table S4 on related functional data from C2C12 cells.

    Article Snippet: ChIP-seq was performed as described previously ( ) using anti-RBFox2 (Bethyl, A300-864A), anti-SUZ12 (Cell Signaling, D39F6), anti-H3K27me3 (Active Motif, 61017), anti-H3K4me3 (Active Motif, 39159) or anti-Pol II (Santa Cruz Biotechnology, sc-899).

    Techniques: Functional Assay, Chromatin Immunoprecipitation

    Deletion of JHD2 restored H3K4me3 levels in cells lacking histone H3 acetylation. ( A ) Whole cell extracts from the indicated strains were subjected to immunoblot analysis for H3K4me3 and H3. A yellow color represented equal red and green intensities.

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

    Article Title: Histone H3K4 demethylation is negatively regulated by histone H3 acetylation in Saccharomyces cerevisiae

    doi: 10.1073/pnas.1202070109

    Figure Lengend Snippet: Deletion of JHD2 restored H3K4me3 levels in cells lacking histone H3 acetylation. ( A ) Whole cell extracts from the indicated strains were subjected to immunoblot analysis for H3K4me3 and H3. A yellow color represented equal red and green intensities.

    Article Snippet: To detect methylation loss, peptides were run on 15% (wt/vol) tricine-SDS-urea gels ( ) and probed with anti-H3K4me3 antibodies (Active Motif, 39159).

    Techniques:

    Histone H3-specific acetyltransferases were required for H3K4me3. ( A and C ) Whole cell extracts from the indicated strains were subjected to immunoblot analysis for H3K4me3, H3K4me2, H3K4me1, H3K4me0, H3K14ac, or H3. ( B and D ) Immunoblots shown in A and

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

    Article Title: Histone H3K4 demethylation is negatively regulated by histone H3 acetylation in Saccharomyces cerevisiae

    doi: 10.1073/pnas.1202070109

    Figure Lengend Snippet: Histone H3-specific acetyltransferases were required for H3K4me3. ( A and C ) Whole cell extracts from the indicated strains were subjected to immunoblot analysis for H3K4me3, H3K4me2, H3K4me1, H3K4me0, H3K14ac, or H3. ( B and D ) Immunoblots shown in A and

    Article Snippet: To detect methylation loss, peptides were run on 15% (wt/vol) tricine-SDS-urea gels ( ) and probed with anti-H3K4me3 antibodies (Active Motif, 39159).

    Techniques: Western Blot

    H3K14ac negatively regulates demethylation by Jhd2 in vivo and in vitro. ( A ) Whole cell extracts were subjected to immunoblot analysis for H3 (red) and H3K4me3 (green) and the images merged. Yellow indicated equal red and green intensities. The strains

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

    Article Title: Histone H3K4 demethylation is negatively regulated by histone H3 acetylation in Saccharomyces cerevisiae

    doi: 10.1073/pnas.1202070109

    Figure Lengend Snippet: H3K14ac negatively regulates demethylation by Jhd2 in vivo and in vitro. ( A ) Whole cell extracts were subjected to immunoblot analysis for H3 (red) and H3K4me3 (green) and the images merged. Yellow indicated equal red and green intensities. The strains

    Article Snippet: To detect methylation loss, peptides were run on 15% (wt/vol) tricine-SDS-urea gels ( ) and probed with anti-H3K4me3 antibodies (Active Motif, 39159).

    Techniques: In Vivo, In Vitro

    KDM5B removes local domains of intragenic H3K4me3. ( A ) Immunoblot analysis of bulk histone modifications from ESCs transfected with control/KDM5B siRNAs. ( B , C ) Genome browser tracks depicting KDM5B ChIP-Seq peaks and H3K4me3 ChIP-Seq peaks from control

    Journal: The EMBO Journal

    Article Title: KDM5B regulates embryonic stem cell self-renewal and represses cryptic intragenic transcription

    doi: 10.1038/emboj.2011.91

    Figure Lengend Snippet: KDM5B removes local domains of intragenic H3K4me3. ( A ) Immunoblot analysis of bulk histone modifications from ESCs transfected with control/KDM5B siRNAs. ( B , C ) Genome browser tracks depicting KDM5B ChIP-Seq peaks and H3K4me3 ChIP-Seq peaks from control

    Article Snippet: Antibodies utilized for ChIP or IP: KDM5B (Abcam ab50958 and Santa Cruz sc-67035), Nanog (Chemicon, AB5731), Oct4 (Santa Cruz, sc-5279), Histone 3 (Abcam, ab1791), H3K4me3 (Active Motif, 39159), H3K36me3 (Abcam, ab9050-100), MRG15 (AVIVA Systems Biology, -T100), non-phosphorylated RNAP (Covance 8GW16), Ser2P RNAP (Abcam ab5095-100 and Covance H5), Ser5P RNAP (Covance H14), WDR5 (Abcam, ab22512-100), and Ash2L (Bethyl A300-112A).

    Techniques: Transfection, Chromatin Immunoprecipitation

    H3K36me3 recruits KDM5B to transcriptionally active intragenic regions. ( A , B ) UCSC genome browser tracks depicting H3K4me3, KDM5B, and H3K36me3 ChIP-Seq peaks at representative gene loci. The numbers on the left axes indicate peak amplitude. ( C ) Histogram

    Journal: The EMBO Journal

    Article Title: KDM5B regulates embryonic stem cell self-renewal and represses cryptic intragenic transcription

    doi: 10.1038/emboj.2011.91

    Figure Lengend Snippet: H3K36me3 recruits KDM5B to transcriptionally active intragenic regions. ( A , B ) UCSC genome browser tracks depicting H3K4me3, KDM5B, and H3K36me3 ChIP-Seq peaks at representative gene loci. The numbers on the left axes indicate peak amplitude. ( C ) Histogram

    Article Snippet: Antibodies utilized for ChIP or IP: KDM5B (Abcam ab50958 and Santa Cruz sc-67035), Nanog (Chemicon, AB5731), Oct4 (Santa Cruz, sc-5279), Histone 3 (Abcam, ab1791), H3K4me3 (Active Motif, 39159), H3K36me3 (Abcam, ab9050-100), MRG15 (AVIVA Systems Biology, -T100), non-phosphorylated RNAP (Covance 8GW16), Ser2P RNAP (Abcam ab5095-100 and Covance H5), Ser5P RNAP (Covance H14), WDR5 (Abcam, ab22512-100), and Ash2L (Bethyl A300-112A).

    Techniques: Chromatin Immunoprecipitation

    KDM5B safeguards transcriptional elongation by repressing cryptic transcription. ( A ) Immunoblot analysis of immunoprecipitated WDR5, Ash2L, Ser5P, and Ser2P with indicated antibodies. ( B ) ChIP-PCR analysis of Ser2P, Ser5P, and H3K4me3 at KDM5B ChIP-Seq

    Journal: The EMBO Journal

    Article Title: KDM5B regulates embryonic stem cell self-renewal and represses cryptic intragenic transcription

    doi: 10.1038/emboj.2011.91

    Figure Lengend Snippet: KDM5B safeguards transcriptional elongation by repressing cryptic transcription. ( A ) Immunoblot analysis of immunoprecipitated WDR5, Ash2L, Ser5P, and Ser2P with indicated antibodies. ( B ) ChIP-PCR analysis of Ser2P, Ser5P, and H3K4me3 at KDM5B ChIP-Seq

    Article Snippet: Antibodies utilized for ChIP or IP: KDM5B (Abcam ab50958 and Santa Cruz sc-67035), Nanog (Chemicon, AB5731), Oct4 (Santa Cruz, sc-5279), Histone 3 (Abcam, ab1791), H3K4me3 (Active Motif, 39159), H3K36me3 (Abcam, ab9050-100), MRG15 (AVIVA Systems Biology, -T100), non-phosphorylated RNAP (Covance 8GW16), Ser2P RNAP (Abcam ab5095-100 and Covance H5), Ser5P RNAP (Covance H14), WDR5 (Abcam, ab22512-100), and Ash2L (Bethyl A300-112A).

    Techniques: Immunoprecipitation, Chromatin Immunoprecipitation, Polymerase Chain Reaction

    FOXF1 modulates enhancer landscape and ETV1 binding to GIST-lineage specific enhancers A , ChIP-seq profile (top) and heatmap (bottom) of ETV1, FOXF1, H3K4me1 and H3K4me3 signal around peak center at enhancers (FOXF1 only: red, FOXF1/ETV1-shared [both]: blue and ETV1-only: green) and at ETV1-bound promoters (purple) with siETV1, siFOXF1, or scramble (siSCR) controls in GIST48 cells. B , Box and whisker plots showing change of ETV1-ChIP-seq (Log 2) by siRNA-mediated downregulation of ETV1 or FOXF1 in GIST48 cells. Box 75%, whiskers 90%. P: Mann-Whitney test d: Cohen size-effect. C , Scatter plots of ETV1-ChIP-seq (Log 2) correlated with FOXF1 ChIP-seq signal (Log 2) by siRNA-mediated downregulation of ETV1 or FOXF1 in GIST48 cells. The ETV1-ChIP-signal change is marked green for ETV1-only, and blue for FOXF1and ETV1-shared (both) enhancer peaks. P: Fisher exact test. D , Representative FOXF1, ETV1 and H3K4me1 ChIP-seq and ATAC-seq profiles at the indicated gene loci with siRNA-mediated perturbation of ETV1 and FOXF1 in GIST48 cells. Gray highlighted the enhancers with appreciable changes in ATAC-seq, and H3K4me1 ChIP-seq signals at the FOXF1-regulated KIT locus, but not in the ETV1-regulated and FOXF1-independent HES1 locus. E , Immunoblots of GIST-T1 and GIST882 cells with exogenous expression of Flag-HA-tagged-ETV1 (HA-ETV1) independent of endogenous FOXF1-mediated transcriptional control under experimental perturbations as indicated. F , ChIP-qRT-PCR signals of HA-ETV1 (α-HA ChIP) at the HES1 enhancer (an ETV1-, but not FOXF1-regulated gene), KIT enhancer (a FOXF1- regulated gene) and PSA control (neither ETV1- nor FOXF1-regulated gene) loci under different conditions as indicated in GIST-T1 and GIST882 cells with exogenous expression of HA-ETV1 as in E . N=3, Mean ± SEM.

    Journal: Cancer discovery

    Article Title: FOXF1 defines the core-regulatory circuitry in gastrointestinal stromal tumor (GIST)

    doi: 10.1158/2159-8290.CD-17-0468

    Figure Lengend Snippet: FOXF1 modulates enhancer landscape and ETV1 binding to GIST-lineage specific enhancers A , ChIP-seq profile (top) and heatmap (bottom) of ETV1, FOXF1, H3K4me1 and H3K4me3 signal around peak center at enhancers (FOXF1 only: red, FOXF1/ETV1-shared [both]: blue and ETV1-only: green) and at ETV1-bound promoters (purple) with siETV1, siFOXF1, or scramble (siSCR) controls in GIST48 cells. B , Box and whisker plots showing change of ETV1-ChIP-seq (Log 2) by siRNA-mediated downregulation of ETV1 or FOXF1 in GIST48 cells. Box 75%, whiskers 90%. P: Mann-Whitney test d: Cohen size-effect. C , Scatter plots of ETV1-ChIP-seq (Log 2) correlated with FOXF1 ChIP-seq signal (Log 2) by siRNA-mediated downregulation of ETV1 or FOXF1 in GIST48 cells. The ETV1-ChIP-signal change is marked green for ETV1-only, and blue for FOXF1and ETV1-shared (both) enhancer peaks. P: Fisher exact test. D , Representative FOXF1, ETV1 and H3K4me1 ChIP-seq and ATAC-seq profiles at the indicated gene loci with siRNA-mediated perturbation of ETV1 and FOXF1 in GIST48 cells. Gray highlighted the enhancers with appreciable changes in ATAC-seq, and H3K4me1 ChIP-seq signals at the FOXF1-regulated KIT locus, but not in the ETV1-regulated and FOXF1-independent HES1 locus. E , Immunoblots of GIST-T1 and GIST882 cells with exogenous expression of Flag-HA-tagged-ETV1 (HA-ETV1) independent of endogenous FOXF1-mediated transcriptional control under experimental perturbations as indicated. F , ChIP-qRT-PCR signals of HA-ETV1 (α-HA ChIP) at the HES1 enhancer (an ETV1-, but not FOXF1-regulated gene), KIT enhancer (a FOXF1- regulated gene) and PSA control (neither ETV1- nor FOXF1-regulated gene) loci under different conditions as indicated in GIST-T1 and GIST882 cells with exogenous expression of HA-ETV1 as in E . N=3, Mean ± SEM.

    Article Snippet: The following primary antibodies were used: rabbit anti-human FOXF1(Abcam, ab168383) for immunoblot, immunoprecipitation, IHC, and ChIP; rabbit anti-ETV1(Abcam; ab184120) for immunoblot, immunoprecipitation and ChIP; rabbit anti-H3K4me3 for ChIP (active motif, 39159); rabbit anti-H3K4me1 for ChIP (Abcam, ab8895); HRP-conjugated anti-beta ACTIN (Abcam, ab49900) for immunoblot; GAPDH (Abcam, ab9385) for immunoblot; rabbit anti-KIT (Cell Signaling Technology, #3074) for immunoblot and IHC; rabbit anti-phospho-c-Kit (Tyr703) (Cell Signaling Technology, #3073); rabbit anti-Akt (pan) (Cell Signaling Technology, #4691); rabbit anti-phospho-Akt (Ser473) (Cell Signaling Technology, #4060); rabbit anti-MEK1/2 (Cell Signaling Technology, #9122), rabbit anti-phospho-MEK1/2 (Ser217/221) (Cell Signaling Technology, #9154); Phospho-Akt (Ser473) (D9E) XP® Rabbit mAb #4060; rabbit anti-Stat3 (Cell Signaling Technology, #12640); rabbit anti-phospho-Stat3 (Tyr705)) (Cell Signaling Technology, #9145); rabbit anti- p44/42 MAPK (Erk1/2) (Cell Signaling Technology, #4695), rabbit anti-phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) Cell Signaling Technology, #4370) for immunoblot; rat anti-mouse Kit (Cedarlane; CL8936ap) for immunofluorescence; APC-conjugated anti-human CD117 (c-kit) (Biolegend, 313205) for FACS; rabbit anti-HA tag (Cell Signaling Technology, #3724) for immunoblot; rabbit anti-HA tag (Abcam, ab9110) for ChIP; rabbit anti-cleaved caspase 3 (Asp175) (Cell Signaling Technology, #9661) for IHC; rabbit anti-Ki67 (Abcam, ab16667) for IHC.

    Techniques: Binding Assay, Chromatin Immunoprecipitation, Whisker Assay, MANN-WHITNEY, Western Blot, Expressing, Quantitative RT-PCR

    Apoptosis is associated with Dot1p-dependent loss of H3K4 methylation and preventing demethylation delays age-dependent cell death. ( A ) Western analysis of wild-type, Δ dot1 , Δset1 , and Δjhd2 cells to monitor H3K4 and H3K79 methylation during chronological aging. Phosphoglycerolkinase (PGK) antibodies were employed as loading control. ( B ) Relative intensity of H3K4me3 and H3K79me3 levels in wild-type cells during chronological aging as determined by densitometry from three independent experiments using Image J software. ( C ) Immunoblot analysis of H3K4 and H3K79 methylation levels in lymphocytes derived from Hutchinson-Gilford progeria syndrome (HGPS) patients at the age of 5, 9 and 13 years, respectively as well as unaffected control donors. ( D ) Survival of wt, Δset1 , and Δjhd2 cells was determined by clonogenicity during chronological aging. Data represent mean ± SD ( n = 3). ( E ) Integrals under the life span curves were determined. Data represent mean ± SD ( n = 3, *P

    Journal: PLoS Genetics

    Article Title: Loss of Histone H3 Methylation at Lysine 4 Triggers Apoptosis in Saccharomyces cerevisiae

    doi: 10.1371/journal.pgen.1004095

    Figure Lengend Snippet: Apoptosis is associated with Dot1p-dependent loss of H3K4 methylation and preventing demethylation delays age-dependent cell death. ( A ) Western analysis of wild-type, Δ dot1 , Δset1 , and Δjhd2 cells to monitor H3K4 and H3K79 methylation during chronological aging. Phosphoglycerolkinase (PGK) antibodies were employed as loading control. ( B ) Relative intensity of H3K4me3 and H3K79me3 levels in wild-type cells during chronological aging as determined by densitometry from three independent experiments using Image J software. ( C ) Immunoblot analysis of H3K4 and H3K79 methylation levels in lymphocytes derived from Hutchinson-Gilford progeria syndrome (HGPS) patients at the age of 5, 9 and 13 years, respectively as well as unaffected control donors. ( D ) Survival of wt, Δset1 , and Δjhd2 cells was determined by clonogenicity during chronological aging. Data represent mean ± SD ( n = 3). ( E ) Integrals under the life span curves were determined. Data represent mean ± SD ( n = 3, *P

    Article Snippet: After SDS-PAGE, proteins were transferred to a PVDF membrane and membranes were probed with the following rabbit polyclonal antibodies: anti-histone H3K4me3 (1∶1000 dilution; 39915, Active Motif), anti-histone H3K4me2 (1∶1000; 39141, Active Motif), anti-histone H3K79me3 (1∶1000; ab2621, Abcam), anti-histone H3 (1∶500; 9715; Cell Signaling), the mouse monoclonal anti-PGK antibody (1∶10.000; Invitrogen) and the respective alkaline-phosphatase conjugated secondary antibodies (1∶20.000; Sigma-Aldrich).

    Techniques: Methylation, Western Blot, Software, Derivative Assay

    Loss of Kdm5/Lid results in high H3K4me3 and abnormal karyosomes independently from the meiotic recombination checkpoint. (A) Schematic representation of Drosophila oogenesis. A germline stem cell produces a cystoblast which undergoes four rounds of pre-meiotic mitosis to form a cyst consisting of 16 cells. In region 2a, up to four cells in a cyst initiate meiosis and form the SC. In region 2b, two cells (pro-oocytes) maintain the meiotic state. By region 3, one of these cells is finally selected as the oocyte, and all other cells have become nurse cells. Karyosome forms at stage 2–3 of oogenesis. At stage 3 and later, the SC gradually disassembles from chromosome arms, except in centromeric regions. At stage 14, the oocyte completes maturation and arrests in meiotic metaphase I. (B) The spatial distribution and quantified level of H3K4me3 in control and Kdm5/lid RNAi oocytes. The total H3K4me3 signal intensity was significantly higher in Kdm5/lid RNAi oocytes at all stages (p

    Journal: PLoS Genetics

    Article Title: Kdm5/Lid Regulates Chromosome Architecture in Meiotic Prophase I Independently of Its Histone Demethylase Activity

    doi: 10.1371/journal.pgen.1006241

    Figure Lengend Snippet: Loss of Kdm5/Lid results in high H3K4me3 and abnormal karyosomes independently from the meiotic recombination checkpoint. (A) Schematic representation of Drosophila oogenesis. A germline stem cell produces a cystoblast which undergoes four rounds of pre-meiotic mitosis to form a cyst consisting of 16 cells. In region 2a, up to four cells in a cyst initiate meiosis and form the SC. In region 2b, two cells (pro-oocytes) maintain the meiotic state. By region 3, one of these cells is finally selected as the oocyte, and all other cells have become nurse cells. Karyosome forms at stage 2–3 of oogenesis. At stage 3 and later, the SC gradually disassembles from chromosome arms, except in centromeric regions. At stage 14, the oocyte completes maturation and arrests in meiotic metaphase I. (B) The spatial distribution and quantified level of H3K4me3 in control and Kdm5/lid RNAi oocytes. The total H3K4me3 signal intensity was significantly higher in Kdm5/lid RNAi oocytes at all stages (p

    Article Snippet: Bickel; [ ]), rat anti-Cid antibody (1/100; this study), rabbit anti-Cid antibody (1/800, Active Motif), rabbit anti-H3K4me3 antibody (1/100; Active Motif), rat monoclonal anti-HA antibody (1/100; 3F10; Roche), mouse monoclonal anti-Hts antibody (1/100; 1B1; Developmental Studies Hybridoma Bank) and mouse monoclonal anti-α-tubulin antibody (1/250; DM1A; Sigma).

    Techniques:

    Kdm5/Lid demethylase activity is dispensable for meiotic chromatin reorganisation. (A) Distribution and intensity of H3K4me3 on meiotic chromosomes in a Kdm5/lid mutant ( lid 10424/k06801 ) without a transgene (–), the Kdm5/lid mutant carrying a wild-type transgene ( lid[WT]) and the Kdm5/lid mutant carrying a catalytically inactive transgene ( lid[JmjC*] ). Images of the karyosome in stage-5 oocytes were taken and the contrast has been enhanced using identical conditions. The total signal intensity of H3K4me3 on the karyosome was measured as described in Materials and Methods. Error bars indicate standard errors. n≥6. The signal intensity in the Kdm5/lid mutant carrying no transgenes (–) or the lid[JmjC*] transgene is significantly different from the one carrying the lid[WT] transgene at all stages (p

    Journal: PLoS Genetics

    Article Title: Kdm5/Lid Regulates Chromosome Architecture in Meiotic Prophase I Independently of Its Histone Demethylase Activity

    doi: 10.1371/journal.pgen.1006241

    Figure Lengend Snippet: Kdm5/Lid demethylase activity is dispensable for meiotic chromatin reorganisation. (A) Distribution and intensity of H3K4me3 on meiotic chromosomes in a Kdm5/lid mutant ( lid 10424/k06801 ) without a transgene (–), the Kdm5/lid mutant carrying a wild-type transgene ( lid[WT]) and the Kdm5/lid mutant carrying a catalytically inactive transgene ( lid[JmjC*] ). Images of the karyosome in stage-5 oocytes were taken and the contrast has been enhanced using identical conditions. The total signal intensity of H3K4me3 on the karyosome was measured as described in Materials and Methods. Error bars indicate standard errors. n≥6. The signal intensity in the Kdm5/lid mutant carrying no transgenes (–) or the lid[JmjC*] transgene is significantly different from the one carrying the lid[WT] transgene at all stages (p

    Article Snippet: Bickel; [ ]), rat anti-Cid antibody (1/100; this study), rabbit anti-Cid antibody (1/800, Active Motif), rabbit anti-H3K4me3 antibody (1/100; Active Motif), rat monoclonal anti-HA antibody (1/100; 3F10; Roche), mouse monoclonal anti-Hts antibody (1/100; 1B1; Developmental Studies Hybridoma Bank) and mouse monoclonal anti-α-tubulin antibody (1/250; DM1A; Sigma).

    Techniques: Activity Assay, Mutagenesis

    Chromatin state of the D H -C H domain of the IgH locus in CD4 + CD8 + DP thymocytes. (A) Top panel shows scale representation of the murine IgH locus based on mm9 (mouse reference genome). V H gene families are indicated in blue. Purple box labeled as DJ contains all D H and J H gene segments, and pink box labeled as C contains exons of all IgH isotypes. The D H -C H domain (120 kb) is expanded below to show the locations of ChIP amplicons (black bars). The intergenic control region 1 (IGCR1), DQ52 promoter (PQ52), and intronic enhancer (Eμ) are regulatory sequences that are marked by DNase I hypersensitive sites in pro-B cells. (B) CD19 + pro-B cells from bone marrow of Rag2 −/− and CD4 + CD8 + thymocytes from TCRβ × Rag2 −/− transgenic mice were used in chromatin immunoprecipitation (ChIP) experiments using anti-H3K4me3 and H3K9ac antibodies. TCF7 and Lck gene promoters served as positive controls in DP thymocytes. Cγ3 was used as a negative control and γ-actin served as a positive control in both cell types. For each independent experiment PCR was done in triplicate. Results shown are the mean of two independent experiments. Error bars represent standard error of the mean ( n = 2). Y-axis shows enrichment of respective amplicons in the immunoprecipitate compared to an equal amount of input DNA as described in the methods. (C) DNase I sensitivity analysis of proximal part of IgH locus in pro-B cells and DP thymocytes. 10 7 nuclei from CD19 + pro-B cells from Rag2 −/− mice and DP thymocytes from TCRβ × Rag2 −/− mice were treated with increasing concentration of DNase I (X-axis) followed by purification of genomic DNA. Equal amounts of DNA were used for amplification with the indicated primers. The signal from each amplicon was normalized to that from a β-globin amplicon for each DNase I concentration. β2m promoter served as a positive control while Cγ3 served as negative control. TCRα enhancer was used as an additional positive control for DP thymocytes. The data represents the mean of two independent experiments. Error bars represent standard error of the mean ( n = 2).

    Journal: Frontiers in Immunology

    Article Title: Misregulation of the IgH Locus in Thymocytes

    doi: 10.3389/fimmu.2018.02426

    Figure Lengend Snippet: Chromatin state of the D H -C H domain of the IgH locus in CD4 + CD8 + DP thymocytes. (A) Top panel shows scale representation of the murine IgH locus based on mm9 (mouse reference genome). V H gene families are indicated in blue. Purple box labeled as DJ contains all D H and J H gene segments, and pink box labeled as C contains exons of all IgH isotypes. The D H -C H domain (120 kb) is expanded below to show the locations of ChIP amplicons (black bars). The intergenic control region 1 (IGCR1), DQ52 promoter (PQ52), and intronic enhancer (Eμ) are regulatory sequences that are marked by DNase I hypersensitive sites in pro-B cells. (B) CD19 + pro-B cells from bone marrow of Rag2 −/− and CD4 + CD8 + thymocytes from TCRβ × Rag2 −/− transgenic mice were used in chromatin immunoprecipitation (ChIP) experiments using anti-H3K4me3 and H3K9ac antibodies. TCF7 and Lck gene promoters served as positive controls in DP thymocytes. Cγ3 was used as a negative control and γ-actin served as a positive control in both cell types. For each independent experiment PCR was done in triplicate. Results shown are the mean of two independent experiments. Error bars represent standard error of the mean ( n = 2). Y-axis shows enrichment of respective amplicons in the immunoprecipitate compared to an equal amount of input DNA as described in the methods. (C) DNase I sensitivity analysis of proximal part of IgH locus in pro-B cells and DP thymocytes. 10 7 nuclei from CD19 + pro-B cells from Rag2 −/− mice and DP thymocytes from TCRβ × Rag2 −/− mice were treated with increasing concentration of DNase I (X-axis) followed by purification of genomic DNA. Equal amounts of DNA were used for amplification with the indicated primers. The signal from each amplicon was normalized to that from a β-globin amplicon for each DNase I concentration. β2m promoter served as a positive control while Cγ3 served as negative control. TCRα enhancer was used as an additional positive control for DP thymocytes. The data represents the mean of two independent experiments. Error bars represent standard error of the mean ( n = 2).

    Article Snippet: Modified histone antibodies were purchased from Active Motif: anti-H3K4me3 (Cat # 39519), anti-H3K9ac (Cat # 39137), anti-H3K27me3 (Cat # 39155).

    Techniques: Labeling, Chromatin Immunoprecipitation, Transgenic Assay, Mouse Assay, Negative Control, Positive Control, Polymerase Chain Reaction, Concentration Assay, Purification, Amplification

    H3K4me3 predicts DNA undermethylation. ( A ) Density scatter plot of H3K4me3 (normalized ChIP-Seq reads) in TKO cells vs. H3K4me3 in WT ES cells. ( B ) Density scatter plot of H3K4me3 (normalized ChIP-Seq reads) in TKO cells vs. percent DNA methylation (normalized RRBS) in WT ES cells. Note that regions marked with H3K4me3 in TKO are unmethylated in WT ES cells. The density of dots is color-coded from blue (low) to red (high).

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

    Article Title: Role of transcription complexes in the formation of the basal methylation pattern in early development

    doi: 10.1073/pnas.1804755115

    Figure Lengend Snippet: H3K4me3 predicts DNA undermethylation. ( A ) Density scatter plot of H3K4me3 (normalized ChIP-Seq reads) in TKO cells vs. H3K4me3 in WT ES cells. ( B ) Density scatter plot of H3K4me3 (normalized ChIP-Seq reads) in TKO cells vs. percent DNA methylation (normalized RRBS) in WT ES cells. Note that regions marked with H3K4me3 in TKO are unmethylated in WT ES cells. The density of dots is color-coded from blue (low) to red (high).

    Article Snippet: Antibodies (5 μg/10–30 μg DNA) were directed against the GAL4 DNA-binding domain (catalog no. 06-262; Millipore), histone H3K4me3 (catalog no. 39160; Active Motif) or RNAP II (catalog no. 17-620; Millipore).

    Techniques: Chromatin Immunoprecipitation, DNA Methylation Assay

    H3K4me3 predicts undermethylation in vivo. Density scatter plot of H3K4me3 (normalized ChIP-Seq reads) in ICM vs. percent DNA methylation (normalized RRBS) in 7.5-d embryos. Dot density is color-coded from blue (low) to red (high).

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

    Article Title: Role of transcription complexes in the formation of the basal methylation pattern in early development

    doi: 10.1073/pnas.1804755115

    Figure Lengend Snippet: H3K4me3 predicts undermethylation in vivo. Density scatter plot of H3K4me3 (normalized ChIP-Seq reads) in ICM vs. percent DNA methylation (normalized RRBS) in 7.5-d embryos. Dot density is color-coded from blue (low) to red (high).

    Article Snippet: Antibodies (5 μg/10–30 μg DNA) were directed against the GAL4 DNA-binding domain (catalog no. 06-262; Millipore), histone H3K4me3 (catalog no. 39160; Active Motif) or RNAP II (catalog no. 17-620; Millipore).

    Techniques: In Vivo, Chromatin Immunoprecipitation, DNA Methylation Assay

    Venn diagrams showing overlap between epigenetic and transcriptional data sets for the top 3CA scores. Transcripts which were preferentially up-regulated with age were compared with down-regulated H3K27me3 regions, down-regulated DNA methylation regions, and up-regulated H3K4me3 regions and vice versa (panels A and B , respectively). Data included are within 1 SD from the best score (top ∼2%).

    Journal: Nucleic Acids Research

    Article Title: Longitudinal epigenetic and gene expression profiles analyzed by three-component analysis reveal down-regulation of genes involved in protein translation in human aging

    doi: 10.1093/nar/gkv473

    Figure Lengend Snippet: Venn diagrams showing overlap between epigenetic and transcriptional data sets for the top 3CA scores. Transcripts which were preferentially up-regulated with age were compared with down-regulated H3K27me3 regions, down-regulated DNA methylation regions, and up-regulated H3K4me3 regions and vice versa (panels A and B , respectively). Data included are within 1 SD from the best score (top ∼2%).

    Article Snippet: Chromatin was immunoprecipitated with antibodies against histone H3K27me3 (Millipore, #07–449), or with anti-histone H3K4me3 antibodies (Active Motif, #39915).

    Techniques: DNA Methylation Assay

    Enrichment of AT-rich motifs following NCD38-β 2 P 4 treatment ( A ) Heat maps showing read densities of H3K27ac within ± 5 kb around H3K27ac-increased regions. ( B ) De novo motif analysis. The motives significantly enriched around H3K27ac-increased regions, Zbtb3_2, Bach1, and ONECUT3, were all AT-rich sequences. ( C ) Expression of genes with enriched motifs. Expression levels of genes nearest to the motives of Zbtb3_2, Bach1, and ONECUT3 with increased H3K27ac levels, were significantly upregulated by NCD38-β 2 P 4 . ( D ) Representative image of SERPINB1 . H3K27ac level was increased at Zbtb3_2 motif site. ( E ) Representative RNA-seq results of SERPINB1 . Expression of SERPINB1 was increased.

    Journal: Oncotarget

    Article Title: Region-specific alteration of histone modification by LSD1 inhibitor conjugated with pyrrole-imidazole polyamide

    doi: 10.18632/oncotarget.25451

    Figure Lengend Snippet: Enrichment of AT-rich motifs following NCD38-β 2 P 4 treatment ( A ) Heat maps showing read densities of H3K27ac within ± 5 kb around H3K27ac-increased regions. ( B ) De novo motif analysis. The motives significantly enriched around H3K27ac-increased regions, Zbtb3_2, Bach1, and ONECUT3, were all AT-rich sequences. ( C ) Expression of genes with enriched motifs. Expression levels of genes nearest to the motives of Zbtb3_2, Bach1, and ONECUT3 with increased H3K27ac levels, were significantly upregulated by NCD38-β 2 P 4 . ( D ) Representative image of SERPINB1 . H3K27ac level was increased at Zbtb3_2 motif site. ( E ) Representative RNA-seq results of SERPINB1 . Expression of SERPINB1 was increased.

    Article Snippet: About 2–5 μg antibody and 20 μL Protein G sepharose beads were mixed in IP dilution buffer and incubated for approximately 6 h at 4° C. Anti-H3K4me2 (#05-1334, Merck Millipore, Billerica, MA, USA), anti-H3K4me3 (#ab7766, Abcam, Cambridge, UK), and anti-H3K27ac (#39159, Active Motif, Carlsbad, CA, USA) antibodies were used in this study.

    Techniques: Expressing, RNA Sequencing Assay

    Appearance of DNA sequences in regions activated by NCD38-β 2 P 4 ( A ) Frequencies of appearance of 6-bp sequences within 250 bp from the center of the increased H3K27ac peaks. All the top 10 sequences were WWWWWW. ( B ) Significant recognition of AT-rich sequences by NCD38-β 2 P 4 . Total of 4,096 6-bp sequences were sorted by the order of frequency of appearance. SSSSSS or 6-bp sequences including five S and one W ( the most left ), or SSSSSS sequences ( second left ), were significantly enriched to the upward ( P

    Journal: Oncotarget

    Article Title: Region-specific alteration of histone modification by LSD1 inhibitor conjugated with pyrrole-imidazole polyamide

    doi: 10.18632/oncotarget.25451

    Figure Lengend Snippet: Appearance of DNA sequences in regions activated by NCD38-β 2 P 4 ( A ) Frequencies of appearance of 6-bp sequences within 250 bp from the center of the increased H3K27ac peaks. All the top 10 sequences were WWWWWW. ( B ) Significant recognition of AT-rich sequences by NCD38-β 2 P 4 . Total of 4,096 6-bp sequences were sorted by the order of frequency of appearance. SSSSSS or 6-bp sequences including five S and one W ( the most left ), or SSSSSS sequences ( second left ), were significantly enriched to the upward ( P

    Article Snippet: About 2–5 μg antibody and 20 μL Protein G sepharose beads were mixed in IP dilution buffer and incubated for approximately 6 h at 4° C. Anti-H3K4me2 (#05-1334, Merck Millipore, Billerica, MA, USA), anti-H3K4me3 (#ab7766, Abcam, Cambridge, UK), and anti-H3K27ac (#39159, Active Motif, Carlsbad, CA, USA) antibodies were used in this study.

    Techniques:

    Distribution of H3K27ac-increased regions following NCD38 treatment ( A ) Pie chart for the distribution of H3K27ac peaks. About half of H3K27ac-increased regions are distributed in promoter regions. ( B ) Heat maps showing read densities of H3K4me2, H3K4me3, and H3K27ac within ± 5 kb around H3K27ac-increased regions in promoter, enhancer, and other regions. Genes nearest to the H3K27ac peaks in promoter, enhancer, and other regions were significantly upregulated ( P = 9 × 10 −5 , P = 0.02, and P = 9 × 10 −8 , respectively).

    Journal: Oncotarget

    Article Title: Region-specific alteration of histone modification by LSD1 inhibitor conjugated with pyrrole-imidazole polyamide

    doi: 10.18632/oncotarget.25451

    Figure Lengend Snippet: Distribution of H3K27ac-increased regions following NCD38 treatment ( A ) Pie chart for the distribution of H3K27ac peaks. About half of H3K27ac-increased regions are distributed in promoter regions. ( B ) Heat maps showing read densities of H3K4me2, H3K4me3, and H3K27ac within ± 5 kb around H3K27ac-increased regions in promoter, enhancer, and other regions. Genes nearest to the H3K27ac peaks in promoter, enhancer, and other regions were significantly upregulated ( P = 9 × 10 −5 , P = 0.02, and P = 9 × 10 −8 , respectively).

    Article Snippet: About 2–5 μg antibody and 20 μL Protein G sepharose beads were mixed in IP dilution buffer and incubated for approximately 6 h at 4° C. Anti-H3K4me2 (#05-1334, Merck Millipore, Billerica, MA, USA), anti-H3K4me3 (#ab7766, Abcam, Cambridge, UK), and anti-H3K27ac (#39159, Active Motif, Carlsbad, CA, USA) antibodies were used in this study.

    Techniques:

    Appearance of DNA sequences in regions activated by NCD38 Frequencies of appearance of 4-bp ( A ) and 6-bp ( B ) DNA sequences within 250 bp from the center of the increased H3K27ac peaks are shown. GC-content of top 10 4-bp sequences was as high as 80% ± 3% (A), and that of top 10 6-bp sequences was also as high as 80% ± 9% (B). ( C ) Less frequent appearance of AT-rich and WWCGWW sequences. Total of 4,096 6-bp sequences were sorted by the order of frequency of appearance, with the most frequent sequence at the top ( #1 ) and the most infrequent sequence at the bottom ( #4096 ). SSSSSS or 6-bp sequences including five S and one W ( left ) were significantly enriched to the upward ( P

    Journal: Oncotarget

    Article Title: Region-specific alteration of histone modification by LSD1 inhibitor conjugated with pyrrole-imidazole polyamide

    doi: 10.18632/oncotarget.25451

    Figure Lengend Snippet: Appearance of DNA sequences in regions activated by NCD38 Frequencies of appearance of 4-bp ( A ) and 6-bp ( B ) DNA sequences within 250 bp from the center of the increased H3K27ac peaks are shown. GC-content of top 10 4-bp sequences was as high as 80% ± 3% (A), and that of top 10 6-bp sequences was also as high as 80% ± 9% (B). ( C ) Less frequent appearance of AT-rich and WWCGWW sequences. Total of 4,096 6-bp sequences were sorted by the order of frequency of appearance, with the most frequent sequence at the top ( #1 ) and the most infrequent sequence at the bottom ( #4096 ). SSSSSS or 6-bp sequences including five S and one W ( left ) were significantly enriched to the upward ( P

    Article Snippet: About 2–5 μg antibody and 20 μL Protein G sepharose beads were mixed in IP dilution buffer and incubated for approximately 6 h at 4° C. Anti-H3K4me2 (#05-1334, Merck Millipore, Billerica, MA, USA), anti-H3K4me3 (#ab7766, Abcam, Cambridge, UK), and anti-H3K27ac (#39159, Active Motif, Carlsbad, CA, USA) antibodies were used in this study.

    Techniques: Sequencing

    Enrichment of GC-rich motifs following NCD38 treatment ( A ) Heat maps showing read densities of H3K27ac within ± 5 kb around H3K27ac-increased regions. ( B ) De novo motif analysis. The motifs significantly enriched around H3K27ac-increased regions, E2F4, IRF8, E2F7, and IRF4, were all GC-rich sequences. ( C ) Expression of genes with the enriched motifs. Expression levels of genes nearest to the motives of E2F4, IRF8, E2F7, and IRF4, with increased H3K27ac levels, were significantly upregulated by NCD38. ( D ) Representative image of DLGAP5 . H3K27ac level was increased at E2F4 motif site. ( E ) Representative RNA-seq results of DLGAP5 . Expression of DLGAP5 was increased.

    Journal: Oncotarget

    Article Title: Region-specific alteration of histone modification by LSD1 inhibitor conjugated with pyrrole-imidazole polyamide

    doi: 10.18632/oncotarget.25451

    Figure Lengend Snippet: Enrichment of GC-rich motifs following NCD38 treatment ( A ) Heat maps showing read densities of H3K27ac within ± 5 kb around H3K27ac-increased regions. ( B ) De novo motif analysis. The motifs significantly enriched around H3K27ac-increased regions, E2F4, IRF8, E2F7, and IRF4, were all GC-rich sequences. ( C ) Expression of genes with the enriched motifs. Expression levels of genes nearest to the motives of E2F4, IRF8, E2F7, and IRF4, with increased H3K27ac levels, were significantly upregulated by NCD38. ( D ) Representative image of DLGAP5 . H3K27ac level was increased at E2F4 motif site. ( E ) Representative RNA-seq results of DLGAP5 . Expression of DLGAP5 was increased.

    Article Snippet: About 2–5 μg antibody and 20 μL Protein G sepharose beads were mixed in IP dilution buffer and incubated for approximately 6 h at 4° C. Anti-H3K4me2 (#05-1334, Merck Millipore, Billerica, MA, USA), anti-H3K4me3 (#ab7766, Abcam, Cambridge, UK), and anti-H3K27ac (#39159, Active Motif, Carlsbad, CA, USA) antibodies were used in this study.

    Techniques: Expressing, RNA Sequencing Assay

    Distribution of H3K27ac-increased regions following NCD38-β 2 P 4 treatment ( A ) Pie chart showing the distribution of H3K27ac peaks. All of the 234 regions were distributed in non-promoter regions. ( B ) Heat maps showing read densities of H3K4me2, H3K4me3, and H3K27ac within ± 5 kb around H3K27ac-increased regions in enhancers and other regions. Genes nearest to the H3K27ac peaks in other regions were significantly upregulated ( P = 9 × 10 −10 ), while those in enhancer regions tended to be upregulated ( P = 0.053).

    Journal: Oncotarget

    Article Title: Region-specific alteration of histone modification by LSD1 inhibitor conjugated with pyrrole-imidazole polyamide

    doi: 10.18632/oncotarget.25451

    Figure Lengend Snippet: Distribution of H3K27ac-increased regions following NCD38-β 2 P 4 treatment ( A ) Pie chart showing the distribution of H3K27ac peaks. All of the 234 regions were distributed in non-promoter regions. ( B ) Heat maps showing read densities of H3K4me2, H3K4me3, and H3K27ac within ± 5 kb around H3K27ac-increased regions in enhancers and other regions. Genes nearest to the H3K27ac peaks in other regions were significantly upregulated ( P = 9 × 10 −10 ), while those in enhancer regions tended to be upregulated ( P = 0.053).

    Article Snippet: About 2–5 μg antibody and 20 μL Protein G sepharose beads were mixed in IP dilution buffer and incubated for approximately 6 h at 4° C. Anti-H3K4me2 (#05-1334, Merck Millipore, Billerica, MA, USA), anti-H3K4me3 (#ab7766, Abcam, Cambridge, UK), and anti-H3K27ac (#39159, Active Motif, Carlsbad, CA, USA) antibodies were used in this study.

    Techniques:

    Alteration of histone modification by NCD38 treatment ( A ) Chemical structure of the LSD1 inhibitor NCD38. ( B ) Heat maps showing the read densities of ChIP-seq within ± 5 kb around the center position of ChIP-seq peaks. Whereas increase of H3K4me3 level was hardly observed, 103 and 458 regions showed > 3-fold increase of H3K4me2 and H3K27ac levels, respectively. Expression of genes nearest to the H3K4me2 and H3K27ac peaks were significantly upregulated ( P = 0.03 and P = 3 × 10 −10 , respectively, t -test).

    Journal: Oncotarget

    Article Title: Region-specific alteration of histone modification by LSD1 inhibitor conjugated with pyrrole-imidazole polyamide

    doi: 10.18632/oncotarget.25451

    Figure Lengend Snippet: Alteration of histone modification by NCD38 treatment ( A ) Chemical structure of the LSD1 inhibitor NCD38. ( B ) Heat maps showing the read densities of ChIP-seq within ± 5 kb around the center position of ChIP-seq peaks. Whereas increase of H3K4me3 level was hardly observed, 103 and 458 regions showed > 3-fold increase of H3K4me2 and H3K27ac levels, respectively. Expression of genes nearest to the H3K4me2 and H3K27ac peaks were significantly upregulated ( P = 0.03 and P = 3 × 10 −10 , respectively, t -test).

    Article Snippet: About 2–5 μg antibody and 20 μL Protein G sepharose beads were mixed in IP dilution buffer and incubated for approximately 6 h at 4° C. Anti-H3K4me2 (#05-1334, Merck Millipore, Billerica, MA, USA), anti-H3K4me3 (#ab7766, Abcam, Cambridge, UK), and anti-H3K27ac (#39159, Active Motif, Carlsbad, CA, USA) antibodies were used in this study.

    Techniques: Modification, Chromatin Immunoprecipitation, Expressing

    Distribution of the H3K27ac-increased regions following NCD38-β 2 PIPP treatment ( A ) Pie chart for the distribution of H3K27ac peaks. Where 9 of the 82 H3K27ac-increased regions (11%) were promoter regions, 73 regions (89%) were distributed in non-promoter regions. ( B ) Heat maps showing read densities of H3K4me2, H3K4me3, and H3K27ac within ± 5 kb around H3K27ac-increased regions. Among the 73 H3K27ac peaks in non-promoter regions, the majority was other regions.

    Journal: Oncotarget

    Article Title: Region-specific alteration of histone modification by LSD1 inhibitor conjugated with pyrrole-imidazole polyamide

    doi: 10.18632/oncotarget.25451

    Figure Lengend Snippet: Distribution of the H3K27ac-increased regions following NCD38-β 2 PIPP treatment ( A ) Pie chart for the distribution of H3K27ac peaks. Where 9 of the 82 H3K27ac-increased regions (11%) were promoter regions, 73 regions (89%) were distributed in non-promoter regions. ( B ) Heat maps showing read densities of H3K4me2, H3K4me3, and H3K27ac within ± 5 kb around H3K27ac-increased regions. Among the 73 H3K27ac peaks in non-promoter regions, the majority was other regions.

    Article Snippet: About 2–5 μg antibody and 20 μL Protein G sepharose beads were mixed in IP dilution buffer and incubated for approximately 6 h at 4° C. Anti-H3K4me2 (#05-1334, Merck Millipore, Billerica, MA, USA), anti-H3K4me3 (#ab7766, Abcam, Cambridge, UK), and anti-H3K27ac (#39159, Active Motif, Carlsbad, CA, USA) antibodies were used in this study.

    Techniques: