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h3k27me3  (EpiCypher)


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    EpiCypher h3k27me3
    (A) Heatmap showing averaged z-scored enrichment of CUT&RUN reads from all three lamin isoforms (lamin), histone modification CUT&RUN (H3K9me2, H3K9me3, <t>H3K27me3,</t> H3K27ac, H3K4me3), and ATAC-seq signal across the six HiLands chromatin states of YSE cells. Lamin enrichment was calculated as fold-change over IgG CUT&RUN prior to z-scoring; histone modification CUT&RUN and ATAC-seq enrichment was z-scored directly. (B) Representative genomic region showing the six HiLands in wild-type YSE cells with genome browser tracks of LADs determined by lamin CUT&RUN enrichment compared to IgG CUT&RUN, histone modification CUT&RUN, and ATAC-seq. Boxed regions highlight fragmented LADs characterized by HiLands-G and -Y. (C) Alluvial plot showing transitions of HiLands-P and HiLands-B LADs in mESCs to their corresponding HiLands in YSE cells. (D) Schematic illustration of the four categories of LADs and non-LADs in mESCs and YSE cells. (E) Representative genomic region illustrating the four categories of LADs and non-LADs in mESCs and YSE cells. Genome browser tracks include published mESC HiLands and LADs mapped by lamin-B1 Dam-ID, as well as hidden-Markov model (HMM)-called mESC LAD annotations generated in this study. Additional tracks include YSE HiLands, YSE HMM-called LAD annotations, and YSE LADs mapped by lamin CUT&RUN all generated in this study. Dashed boxes indicate examples of YSE-specific non-LADs, shared LADs, YSE-specific LAD regions, and shared non-LADs. (F) Representative fragmented YSE-specific LAD regions (dashed boxes). Genome browser tracks include published mESC LADs mapped by lamin-B1 Dam-ID and HiLands, along with YSE HiLands, LADs mapped by lamin CUT&RUN, ATAC-seq, H3K27ac CUT&RUN, and H3K27me3 CUT&RUN generated in this study. (G) Zoomed-in view of the gray highlighted region in (F) showing an example expressed YSE gene involved in lipid metabolism within HiLands-R and a repressed broad-lineage gene within HiLands-O regions that interrupt YSE-specific LADs. Genome browser tracks include YSE HiLands, ATAC-seq, RNA-seq, as well as H3K27ac and H3K27me3 CUT&RUN generated in this study. (H) Representative YSE-specific non-LAD (dashed boxed) containing the highly expressed YSE gene Afp . Genome browser tracks include published mESC LADs mapped by lamin-B1 Dam-ID and HiLands, along with YSE HiLands, LADs mapped by lamin CUT&RUN, ATAC-seq, and RNA-seq generated in this study. (I) Enrichment of binding motifs for YSE-relevant transcription factors in YSE ATAC-seq peaks associated with shared LADs, YSE-specific non-LADs, and YSE-specific LAD regions.
    H3k27me3, supplied by EpiCypher, used in various techniques. Bioz Stars score: 95/100, based on 41 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/13-0055/H3K27me3+Antibody%2C+SNAP-Certified+for+CUT%26RUN+and+CUT%26Tag/bio_rxiv__64898__2026__04__30__722071-374-29-30
    Average 95 stars, based on 41 article reviews
    h3k27me3 - by Bioz Stars, 2026-10
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    Images

    1) Product Images from "Lamins and lineage-relevant transcription factors coordinate gene expression in lineage development"

    Article Title: Lamins and lineage-relevant transcription factors coordinate gene expression in lineage development

    Journal: bioRxiv

    doi: 10.64898/2026.04.30.722071

    (A) Heatmap showing averaged z-scored enrichment of CUT&RUN reads from all three lamin isoforms (lamin), histone modification CUT&RUN (H3K9me2, H3K9me3, H3K27me3, H3K27ac, H3K4me3), and ATAC-seq signal across the six HiLands chromatin states of YSE cells. Lamin enrichment was calculated as fold-change over IgG CUT&RUN prior to z-scoring; histone modification CUT&RUN and ATAC-seq enrichment was z-scored directly. (B) Representative genomic region showing the six HiLands in wild-type YSE cells with genome browser tracks of LADs determined by lamin CUT&RUN enrichment compared to IgG CUT&RUN, histone modification CUT&RUN, and ATAC-seq. Boxed regions highlight fragmented LADs characterized by HiLands-G and -Y. (C) Alluvial plot showing transitions of HiLands-P and HiLands-B LADs in mESCs to their corresponding HiLands in YSE cells. (D) Schematic illustration of the four categories of LADs and non-LADs in mESCs and YSE cells. (E) Representative genomic region illustrating the four categories of LADs and non-LADs in mESCs and YSE cells. Genome browser tracks include published mESC HiLands and LADs mapped by lamin-B1 Dam-ID, as well as hidden-Markov model (HMM)-called mESC LAD annotations generated in this study. Additional tracks include YSE HiLands, YSE HMM-called LAD annotations, and YSE LADs mapped by lamin CUT&RUN all generated in this study. Dashed boxes indicate examples of YSE-specific non-LADs, shared LADs, YSE-specific LAD regions, and shared non-LADs. (F) Representative fragmented YSE-specific LAD regions (dashed boxes). Genome browser tracks include published mESC LADs mapped by lamin-B1 Dam-ID and HiLands, along with YSE HiLands, LADs mapped by lamin CUT&RUN, ATAC-seq, H3K27ac CUT&RUN, and H3K27me3 CUT&RUN generated in this study. (G) Zoomed-in view of the gray highlighted region in (F) showing an example expressed YSE gene involved in lipid metabolism within HiLands-R and a repressed broad-lineage gene within HiLands-O regions that interrupt YSE-specific LADs. Genome browser tracks include YSE HiLands, ATAC-seq, RNA-seq, as well as H3K27ac and H3K27me3 CUT&RUN generated in this study. (H) Representative YSE-specific non-LAD (dashed boxed) containing the highly expressed YSE gene Afp . Genome browser tracks include published mESC LADs mapped by lamin-B1 Dam-ID and HiLands, along with YSE HiLands, LADs mapped by lamin CUT&RUN, ATAC-seq, and RNA-seq generated in this study. (I) Enrichment of binding motifs for YSE-relevant transcription factors in YSE ATAC-seq peaks associated with shared LADs, YSE-specific non-LADs, and YSE-specific LAD regions.
    Figure Legend Snippet: (A) Heatmap showing averaged z-scored enrichment of CUT&RUN reads from all three lamin isoforms (lamin), histone modification CUT&RUN (H3K9me2, H3K9me3, H3K27me3, H3K27ac, H3K4me3), and ATAC-seq signal across the six HiLands chromatin states of YSE cells. Lamin enrichment was calculated as fold-change over IgG CUT&RUN prior to z-scoring; histone modification CUT&RUN and ATAC-seq enrichment was z-scored directly. (B) Representative genomic region showing the six HiLands in wild-type YSE cells with genome browser tracks of LADs determined by lamin CUT&RUN enrichment compared to IgG CUT&RUN, histone modification CUT&RUN, and ATAC-seq. Boxed regions highlight fragmented LADs characterized by HiLands-G and -Y. (C) Alluvial plot showing transitions of HiLands-P and HiLands-B LADs in mESCs to their corresponding HiLands in YSE cells. (D) Schematic illustration of the four categories of LADs and non-LADs in mESCs and YSE cells. (E) Representative genomic region illustrating the four categories of LADs and non-LADs in mESCs and YSE cells. Genome browser tracks include published mESC HiLands and LADs mapped by lamin-B1 Dam-ID, as well as hidden-Markov model (HMM)-called mESC LAD annotations generated in this study. Additional tracks include YSE HiLands, YSE HMM-called LAD annotations, and YSE LADs mapped by lamin CUT&RUN all generated in this study. Dashed boxes indicate examples of YSE-specific non-LADs, shared LADs, YSE-specific LAD regions, and shared non-LADs. (F) Representative fragmented YSE-specific LAD regions (dashed boxes). Genome browser tracks include published mESC LADs mapped by lamin-B1 Dam-ID and HiLands, along with YSE HiLands, LADs mapped by lamin CUT&RUN, ATAC-seq, H3K27ac CUT&RUN, and H3K27me3 CUT&RUN generated in this study. (G) Zoomed-in view of the gray highlighted region in (F) showing an example expressed YSE gene involved in lipid metabolism within HiLands-R and a repressed broad-lineage gene within HiLands-O regions that interrupt YSE-specific LADs. Genome browser tracks include YSE HiLands, ATAC-seq, RNA-seq, as well as H3K27ac and H3K27me3 CUT&RUN generated in this study. (H) Representative YSE-specific non-LAD (dashed boxed) containing the highly expressed YSE gene Afp . Genome browser tracks include published mESC LADs mapped by lamin-B1 Dam-ID and HiLands, along with YSE HiLands, LADs mapped by lamin CUT&RUN, ATAC-seq, and RNA-seq generated in this study. (I) Enrichment of binding motifs for YSE-relevant transcription factors in YSE ATAC-seq peaks associated with shared LADs, YSE-specific non-LADs, and YSE-specific LAD regions.

    Techniques Used: Modification, Generated, RNA Sequencing, Binding Assay

    (A and B) Metaplots of H3K27ac CUT&RUN signal around promoters of downregulated genes associated with binding motifs of YSE-relevant transcription factors (A) and H3K27me3 CUT&RUN signal around promoters of upregulated genes associated with binding motifs of YSE-relevant transcriptions (B) in the indicated LAD and non-LAD regions. (C) Genome browser view of ATAC-seq peaks and GATA4/6 binding motifs around the upregulated broad-lineage gene Cxcl12 , alongside tracks of bulk RNA-seq and H3K27me3 CUT&RUN from control and lamin-A/B1 DKO cells. An ATAC-seq peak containing GATA4/6 motifs is highlighted (dashed box). (D) Heatmap showing 3D chromatin interaction changes around Cxcl12 upon lamin-A/B1 loss. Boxed regions and arrows highlight increased interactions with transcriptionally active HiLands-R and reduced interactions with repressive HiLands-B. (E) Genome browser view of ATAC-seq and HNF4α binding motifs around the downregulated gene Afp with known functions in YSE cells, alongside tracks of bulk RNA-seq and H3K27ac CUT&RUN from control and lamin-A/B1 DKO cells. ATAC-seq peaks containing HNF4α motifs are highlighted (dashed box). (F) Heatmap showing 3D chromatin interaction changes around Afp upon lamin-A/B1 loss. Boxed regions and arrows indicate increased interactions with repressive HiLands-B. (G and H) Heatmaps of observed/expected (O/E) Hi-C interactions of the zoomed-in region around Afp outlined by the dashed box in (F) of control (G) and lamin-A/B1 DKO (H) YSE cells. The boxed region and arrows highlight reduced interactions between Afp and transcriptionally active HiLands-R upon lamin-A/B1 loss.
    Figure Legend Snippet: (A and B) Metaplots of H3K27ac CUT&RUN signal around promoters of downregulated genes associated with binding motifs of YSE-relevant transcription factors (A) and H3K27me3 CUT&RUN signal around promoters of upregulated genes associated with binding motifs of YSE-relevant transcriptions (B) in the indicated LAD and non-LAD regions. (C) Genome browser view of ATAC-seq peaks and GATA4/6 binding motifs around the upregulated broad-lineage gene Cxcl12 , alongside tracks of bulk RNA-seq and H3K27me3 CUT&RUN from control and lamin-A/B1 DKO cells. An ATAC-seq peak containing GATA4/6 motifs is highlighted (dashed box). (D) Heatmap showing 3D chromatin interaction changes around Cxcl12 upon lamin-A/B1 loss. Boxed regions and arrows highlight increased interactions with transcriptionally active HiLands-R and reduced interactions with repressive HiLands-B. (E) Genome browser view of ATAC-seq and HNF4α binding motifs around the downregulated gene Afp with known functions in YSE cells, alongside tracks of bulk RNA-seq and H3K27ac CUT&RUN from control and lamin-A/B1 DKO cells. ATAC-seq peaks containing HNF4α motifs are highlighted (dashed box). (F) Heatmap showing 3D chromatin interaction changes around Afp upon lamin-A/B1 loss. Boxed regions and arrows indicate increased interactions with repressive HiLands-B. (G and H) Heatmaps of observed/expected (O/E) Hi-C interactions of the zoomed-in region around Afp outlined by the dashed box in (F) of control (G) and lamin-A/B1 DKO (H) YSE cells. The boxed region and arrows highlight reduced interactions between Afp and transcriptionally active HiLands-R upon lamin-A/B1 loss.

    Techniques Used: Binding Assay, RNA Sequencing, Control, Hi-C

    Related Articles

    Activation Assay:

    Article Title: Increased Glycine-N-methyltransferase expression disrupts light-dependent gene expression rhythms in the Drosophila eye.
    Article Snippet: .. The following antibodies were used for CUT&RUN with 20 min of pAG-MNase activation time: anti-IgG (EpiCypher, 13-0042; RRID:AB_ 2923178), anti-H3K4me3 (EpiCypher, 13-0060), anti-H3K4me1 (Abcam, ab8895; RRID:AB_306847), anti-H3K9me3 (Abcam, ab176916; RRID: AB_2797591), anti-H3K27me3 (EpiCypher, 13-0055; RRID:AB_3665059). .. RNA was extracted from five larvae using the Zymoprep Direct-zol RNA MicroPrep kit (Zymo Research, R2050).

    Western Blot:

    Article Title: Histone H4 acetyl-methyllysine marks accessible chromatin that resists compaction
    Article Snippet: Unless otherwise indicated in the figure captions, experiments targeting KDM6A/B were performed by treating HEK293T cells with 5 μM GSK-J4 (MCE, HY-15648B) for either 6 or 24 hrs. .. The following antibodies were used: anti-Kacme (developed with Abcam; 1:1,000 (Western blots), 2.0 μg per rxn (ChIP-seq), 0.5 μg per rxn (CUT&RUN), and 1:1,000 (IF)); anti-H4Kacme (developed with Cocalico Biologicals; 1:1,000 (Western blots) and 2.0 μg per rxn (ChIP-seq); anti-H3K27me3 (EpiCypher, 13-0055, 1:10,000 (Western blots) and 0.5 μg per rxn (CUT&RUN)); anti-H3K4me3 (EpiCypher, 13-0060, 0.5 μg per rxn (CUT&RUN)); anti-H3K27ac (Abcam, ab4729, 2.0 μg per rxn (ChIP-seq)); anti-CTCF (Active Motif, 61311, 1.0 μg per rxn (CUT&RUN)); anti-H4Kac (Abcam, ab233193, 2.0 μg per rxn (ChIP-seq)); anti-H4K5ac (Millipore, 07-327, 1:2,000 (Western blots), 2.0 μg per rxn (ChIP-seq), and 0.5 μg per rxn (CUT&RUN); anti-Histone H3 (phospho S10) (Abcam, ab47297, 1:500 (Western blots)); anti-ACA(Antibodies Inc., 15-234-0001, 1:1,000); anti-IgG negative control (EpiCypher, 13-0042, 0.5 μg per rxn (CUT&RUN)); goat anti-rabbit IgG-HRP (Invitrogen, 31460, 1:2,000 (Western blots)); Alexa Fluor AffiniPure goat anti-rabbit IgG (H+L) (Jackson ImmunoResearch, 1:1,000). .. Histone extracts were collected using the EpiQuik Total Histone Extraction Kit (Epigentek) following the standard kit instructions.

    Chromatin Immunoprecipitation:

    Article Title: Histone H4 acetyl-methyllysine marks accessible chromatin that resists compaction
    Article Snippet: Unless otherwise indicated in the figure captions, experiments targeting KDM6A/B were performed by treating HEK293T cells with 5 μM GSK-J4 (MCE, HY-15648B) for either 6 or 24 hrs. .. The following antibodies were used: anti-Kacme (developed with Abcam; 1:1,000 (Western blots), 2.0 μg per rxn (ChIP-seq), 0.5 μg per rxn (CUT&RUN), and 1:1,000 (IF)); anti-H4Kacme (developed with Cocalico Biologicals; 1:1,000 (Western blots) and 2.0 μg per rxn (ChIP-seq); anti-H3K27me3 (EpiCypher, 13-0055, 1:10,000 (Western blots) and 0.5 μg per rxn (CUT&RUN)); anti-H3K4me3 (EpiCypher, 13-0060, 0.5 μg per rxn (CUT&RUN)); anti-H3K27ac (Abcam, ab4729, 2.0 μg per rxn (ChIP-seq)); anti-CTCF (Active Motif, 61311, 1.0 μg per rxn (CUT&RUN)); anti-H4Kac (Abcam, ab233193, 2.0 μg per rxn (ChIP-seq)); anti-H4K5ac (Millipore, 07-327, 1:2,000 (Western blots), 2.0 μg per rxn (ChIP-seq), and 0.5 μg per rxn (CUT&RUN); anti-Histone H3 (phospho S10) (Abcam, ab47297, 1:500 (Western blots)); anti-ACA(Antibodies Inc., 15-234-0001, 1:1,000); anti-IgG negative control (EpiCypher, 13-0042, 0.5 μg per rxn (CUT&RUN)); goat anti-rabbit IgG-HRP (Invitrogen, 31460, 1:2,000 (Western blots)); Alexa Fluor AffiniPure goat anti-rabbit IgG (H+L) (Jackson ImmunoResearch, 1:1,000). .. Histone extracts were collected using the EpiQuik Total Histone Extraction Kit (Epigentek) following the standard kit instructions.

    Negative Control:

    Article Title: Histone H4 acetyl-methyllysine marks accessible chromatin that resists compaction
    Article Snippet: Unless otherwise indicated in the figure captions, experiments targeting KDM6A/B were performed by treating HEK293T cells with 5 μM GSK-J4 (MCE, HY-15648B) for either 6 or 24 hrs. .. The following antibodies were used: anti-Kacme (developed with Abcam; 1:1,000 (Western blots), 2.0 μg per rxn (ChIP-seq), 0.5 μg per rxn (CUT&RUN), and 1:1,000 (IF)); anti-H4Kacme (developed with Cocalico Biologicals; 1:1,000 (Western blots) and 2.0 μg per rxn (ChIP-seq); anti-H3K27me3 (EpiCypher, 13-0055, 1:10,000 (Western blots) and 0.5 μg per rxn (CUT&RUN)); anti-H3K4me3 (EpiCypher, 13-0060, 0.5 μg per rxn (CUT&RUN)); anti-H3K27ac (Abcam, ab4729, 2.0 μg per rxn (ChIP-seq)); anti-CTCF (Active Motif, 61311, 1.0 μg per rxn (CUT&RUN)); anti-H4Kac (Abcam, ab233193, 2.0 μg per rxn (ChIP-seq)); anti-H4K5ac (Millipore, 07-327, 1:2,000 (Western blots), 2.0 μg per rxn (ChIP-seq), and 0.5 μg per rxn (CUT&RUN); anti-Histone H3 (phospho S10) (Abcam, ab47297, 1:500 (Western blots)); anti-ACA(Antibodies Inc., 15-234-0001, 1:1,000); anti-IgG negative control (EpiCypher, 13-0042, 0.5 μg per rxn (CUT&RUN)); goat anti-rabbit IgG-HRP (Invitrogen, 31460, 1:2,000 (Western blots)); Alexa Fluor AffiniPure goat anti-rabbit IgG (H+L) (Jackson ImmunoResearch, 1:1,000). .. Histone extracts were collected using the EpiQuik Total Histone Extraction Kit (Epigentek) following the standard kit instructions.

    other:

    Article Title: Multiomic screening platform uncovers the impact of histone mutations on chromatin and cell fate
    Article Snippet: CUT&RUN was subsequently performed using the CUTANA ChIC/CUT&RUN Kit (Epicypher, 14-1048).



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    (A) Heatmap showing averaged z-scored enrichment of CUT&RUN reads from all three lamin isoforms (lamin), histone modification CUT&RUN (H3K9me2, H3K9me3, <t>H3K27me3,</t> H3K27ac, H3K4me3), and ATAC-seq signal across the six HiLands chromatin states of YSE cells. Lamin enrichment was calculated as fold-change over IgG CUT&RUN prior to z-scoring; histone modification CUT&RUN and ATAC-seq enrichment was z-scored directly. (B) Representative genomic region showing the six HiLands in wild-type YSE cells with genome browser tracks of LADs determined by lamin CUT&RUN enrichment compared to IgG CUT&RUN, histone modification CUT&RUN, and ATAC-seq. Boxed regions highlight fragmented LADs characterized by HiLands-G and -Y. (C) Alluvial plot showing transitions of HiLands-P and HiLands-B LADs in mESCs to their corresponding HiLands in YSE cells. (D) Schematic illustration of the four categories of LADs and non-LADs in mESCs and YSE cells. (E) Representative genomic region illustrating the four categories of LADs and non-LADs in mESCs and YSE cells. Genome browser tracks include published mESC HiLands and LADs mapped by lamin-B1 Dam-ID, as well as hidden-Markov model (HMM)-called mESC LAD annotations generated in this study. Additional tracks include YSE HiLands, YSE HMM-called LAD annotations, and YSE LADs mapped by lamin CUT&RUN all generated in this study. Dashed boxes indicate examples of YSE-specific non-LADs, shared LADs, YSE-specific LAD regions, and shared non-LADs. (F) Representative fragmented YSE-specific LAD regions (dashed boxes). Genome browser tracks include published mESC LADs mapped by lamin-B1 Dam-ID and HiLands, along with YSE HiLands, LADs mapped by lamin CUT&RUN, ATAC-seq, H3K27ac CUT&RUN, and H3K27me3 CUT&RUN generated in this study. (G) Zoomed-in view of the gray highlighted region in (F) showing an example expressed YSE gene involved in lipid metabolism within HiLands-R and a repressed broad-lineage gene within HiLands-O regions that interrupt YSE-specific LADs. Genome browser tracks include YSE HiLands, ATAC-seq, RNA-seq, as well as H3K27ac and H3K27me3 CUT&RUN generated in this study. (H) Representative YSE-specific non-LAD (dashed boxed) containing the highly expressed YSE gene Afp . Genome browser tracks include published mESC LADs mapped by lamin-B1 Dam-ID and HiLands, along with YSE HiLands, LADs mapped by lamin CUT&RUN, ATAC-seq, and RNA-seq generated in this study. (I) Enrichment of binding motifs for YSE-relevant transcription factors in YSE ATAC-seq peaks associated with shared LADs, YSE-specific non-LADs, and YSE-specific LAD regions.
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    95
    EpiCypher h3k27me3 antibody, snap-certified™ for cut&run and cut&tag
    (A) Heatmap showing averaged z-scored enrichment of CUT&RUN reads from all three lamin isoforms (lamin), histone modification CUT&RUN (H3K9me2, H3K9me3, <t>H3K27me3,</t> H3K27ac, H3K4me3), and ATAC-seq signal across the six HiLands chromatin states of YSE cells. Lamin enrichment was calculated as fold-change over IgG CUT&RUN prior to z-scoring; histone modification CUT&RUN and ATAC-seq enrichment was z-scored directly. (B) Representative genomic region showing the six HiLands in wild-type YSE cells with genome browser tracks of LADs determined by lamin CUT&RUN enrichment compared to IgG CUT&RUN, histone modification CUT&RUN, and ATAC-seq. Boxed regions highlight fragmented LADs characterized by HiLands-G and -Y. (C) Alluvial plot showing transitions of HiLands-P and HiLands-B LADs in mESCs to their corresponding HiLands in YSE cells. (D) Schematic illustration of the four categories of LADs and non-LADs in mESCs and YSE cells. (E) Representative genomic region illustrating the four categories of LADs and non-LADs in mESCs and YSE cells. Genome browser tracks include published mESC HiLands and LADs mapped by lamin-B1 Dam-ID, as well as hidden-Markov model (HMM)-called mESC LAD annotations generated in this study. Additional tracks include YSE HiLands, YSE HMM-called LAD annotations, and YSE LADs mapped by lamin CUT&RUN all generated in this study. Dashed boxes indicate examples of YSE-specific non-LADs, shared LADs, YSE-specific LAD regions, and shared non-LADs. (F) Representative fragmented YSE-specific LAD regions (dashed boxes). Genome browser tracks include published mESC LADs mapped by lamin-B1 Dam-ID and HiLands, along with YSE HiLands, LADs mapped by lamin CUT&RUN, ATAC-seq, H3K27ac CUT&RUN, and H3K27me3 CUT&RUN generated in this study. (G) Zoomed-in view of the gray highlighted region in (F) showing an example expressed YSE gene involved in lipid metabolism within HiLands-R and a repressed broad-lineage gene within HiLands-O regions that interrupt YSE-specific LADs. Genome browser tracks include YSE HiLands, ATAC-seq, RNA-seq, as well as H3K27ac and H3K27me3 CUT&RUN generated in this study. (H) Representative YSE-specific non-LAD (dashed boxed) containing the highly expressed YSE gene Afp . Genome browser tracks include published mESC LADs mapped by lamin-B1 Dam-ID and HiLands, along with YSE HiLands, LADs mapped by lamin CUT&RUN, ATAC-seq, and RNA-seq generated in this study. (I) Enrichment of binding motifs for YSE-relevant transcription factors in YSE ATAC-seq peaks associated with shared LADs, YSE-specific non-LADs, and YSE-specific LAD regions.
    H3k27me3 Antibody, Snap Certified™ For Cut&Run And Cut&Tag, supplied by EpiCypher, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    h3k4me1  (EpiCypher)
    95
    EpiCypher h3k4me1
    (A) Genome-wide matrix of topologically associated domains (TADs) shows that most interactions are intrachromosomal (diagonal intensity pattern indicates each chromosome plotted against itself). A unique interaction pattern between chromosomes 1p and 7q (black arrow) was observed in KT-47R1 but not in KT-47PT. (B) Hi-C identified an interchromosomal interaction between chromosome 1p32.3 ( GLIS1 locus) and chromosome 7q21 ( ABCB1 locus, black arrow) in KT-47R1. The light red vertical line marks the boundary between interacting regions of chromosomes 1 (right) and 7 (left). Red arcs indicate interactions between chromosomes 1 and 7 in KT-47R1, absent in KT-47PT (no blue arcs crossing the boundary). RNA-seq reads confirm upregulation of ABCB1 (black arrow) in KT-47R1. (C) CUT&Tag analysis shows <t>H3K4me1</t> peaks within the interacting region of chromosome 1p32.3. Peaks are present in both KT-47PT and KT-47R1, but the chromatin interaction occurs only in KT-47R1. (D) FISH 1p32.3 break-apart analysis demonstrates no translocation involving 1p32.3 in KT-47PT, KT-47 pre-resistance, KT-47R1, or KT-47R2. Scale bars, 5 μm. (E) Chromosome 1 and 7 painting analysis indicated increased interaction (colocalization) between chromosomes 1 and 7 in KT-47R1 (48%) and KT-47R2 (48%) when compared to KT-47PT (19%) and KT-47PR (25%). Scale bars, 10 μm. n = 2 samples per group.
    H3k4me1, supplied by EpiCypher, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    (A) Heatmap showing averaged z-scored enrichment of CUT&RUN reads from all three lamin isoforms (lamin), histone modification CUT&RUN (H3K9me2, H3K9me3, H3K27me3, H3K27ac, H3K4me3), and ATAC-seq signal across the six HiLands chromatin states of YSE cells. Lamin enrichment was calculated as fold-change over IgG CUT&RUN prior to z-scoring; histone modification CUT&RUN and ATAC-seq enrichment was z-scored directly. (B) Representative genomic region showing the six HiLands in wild-type YSE cells with genome browser tracks of LADs determined by lamin CUT&RUN enrichment compared to IgG CUT&RUN, histone modification CUT&RUN, and ATAC-seq. Boxed regions highlight fragmented LADs characterized by HiLands-G and -Y. (C) Alluvial plot showing transitions of HiLands-P and HiLands-B LADs in mESCs to their corresponding HiLands in YSE cells. (D) Schematic illustration of the four categories of LADs and non-LADs in mESCs and YSE cells. (E) Representative genomic region illustrating the four categories of LADs and non-LADs in mESCs and YSE cells. Genome browser tracks include published mESC HiLands and LADs mapped by lamin-B1 Dam-ID, as well as hidden-Markov model (HMM)-called mESC LAD annotations generated in this study. Additional tracks include YSE HiLands, YSE HMM-called LAD annotations, and YSE LADs mapped by lamin CUT&RUN all generated in this study. Dashed boxes indicate examples of YSE-specific non-LADs, shared LADs, YSE-specific LAD regions, and shared non-LADs. (F) Representative fragmented YSE-specific LAD regions (dashed boxes). Genome browser tracks include published mESC LADs mapped by lamin-B1 Dam-ID and HiLands, along with YSE HiLands, LADs mapped by lamin CUT&RUN, ATAC-seq, H3K27ac CUT&RUN, and H3K27me3 CUT&RUN generated in this study. (G) Zoomed-in view of the gray highlighted region in (F) showing an example expressed YSE gene involved in lipid metabolism within HiLands-R and a repressed broad-lineage gene within HiLands-O regions that interrupt YSE-specific LADs. Genome browser tracks include YSE HiLands, ATAC-seq, RNA-seq, as well as H3K27ac and H3K27me3 CUT&RUN generated in this study. (H) Representative YSE-specific non-LAD (dashed boxed) containing the highly expressed YSE gene Afp . Genome browser tracks include published mESC LADs mapped by lamin-B1 Dam-ID and HiLands, along with YSE HiLands, LADs mapped by lamin CUT&RUN, ATAC-seq, and RNA-seq generated in this study. (I) Enrichment of binding motifs for YSE-relevant transcription factors in YSE ATAC-seq peaks associated with shared LADs, YSE-specific non-LADs, and YSE-specific LAD regions.

    Journal: bioRxiv

    Article Title: Lamins and lineage-relevant transcription factors coordinate gene expression in lineage development

    doi: 10.64898/2026.04.30.722071

    Figure Lengend Snippet: (A) Heatmap showing averaged z-scored enrichment of CUT&RUN reads from all three lamin isoforms (lamin), histone modification CUT&RUN (H3K9me2, H3K9me3, H3K27me3, H3K27ac, H3K4me3), and ATAC-seq signal across the six HiLands chromatin states of YSE cells. Lamin enrichment was calculated as fold-change over IgG CUT&RUN prior to z-scoring; histone modification CUT&RUN and ATAC-seq enrichment was z-scored directly. (B) Representative genomic region showing the six HiLands in wild-type YSE cells with genome browser tracks of LADs determined by lamin CUT&RUN enrichment compared to IgG CUT&RUN, histone modification CUT&RUN, and ATAC-seq. Boxed regions highlight fragmented LADs characterized by HiLands-G and -Y. (C) Alluvial plot showing transitions of HiLands-P and HiLands-B LADs in mESCs to their corresponding HiLands in YSE cells. (D) Schematic illustration of the four categories of LADs and non-LADs in mESCs and YSE cells. (E) Representative genomic region illustrating the four categories of LADs and non-LADs in mESCs and YSE cells. Genome browser tracks include published mESC HiLands and LADs mapped by lamin-B1 Dam-ID, as well as hidden-Markov model (HMM)-called mESC LAD annotations generated in this study. Additional tracks include YSE HiLands, YSE HMM-called LAD annotations, and YSE LADs mapped by lamin CUT&RUN all generated in this study. Dashed boxes indicate examples of YSE-specific non-LADs, shared LADs, YSE-specific LAD regions, and shared non-LADs. (F) Representative fragmented YSE-specific LAD regions (dashed boxes). Genome browser tracks include published mESC LADs mapped by lamin-B1 Dam-ID and HiLands, along with YSE HiLands, LADs mapped by lamin CUT&RUN, ATAC-seq, H3K27ac CUT&RUN, and H3K27me3 CUT&RUN generated in this study. (G) Zoomed-in view of the gray highlighted region in (F) showing an example expressed YSE gene involved in lipid metabolism within HiLands-R and a repressed broad-lineage gene within HiLands-O regions that interrupt YSE-specific LADs. Genome browser tracks include YSE HiLands, ATAC-seq, RNA-seq, as well as H3K27ac and H3K27me3 CUT&RUN generated in this study. (H) Representative YSE-specific non-LAD (dashed boxed) containing the highly expressed YSE gene Afp . Genome browser tracks include published mESC LADs mapped by lamin-B1 Dam-ID and HiLands, along with YSE HiLands, LADs mapped by lamin CUT&RUN, ATAC-seq, and RNA-seq generated in this study. (I) Enrichment of binding motifs for YSE-relevant transcription factors in YSE ATAC-seq peaks associated with shared LADs, YSE-specific non-LADs, and YSE-specific LAD regions.

    Article Snippet: The following antibodies were used for additional CUT&RUN: Lamin-A/C (Abcam, ab133256), Lamin-B1 (Abcam, ab16048), Lamin-B2 (Abcam, ab138516), H3K9me2 (Diagenode, C15200154), H3K9me3 (Active Motif, Cat. no. 39062), H3K27ac (Epicypher, 13–0059), H3K27me3 (Epicypher, 13-0055).

    Techniques: Modification, Generated, RNA Sequencing, Binding Assay

    (A and B) Metaplots of H3K27ac CUT&RUN signal around promoters of downregulated genes associated with binding motifs of YSE-relevant transcription factors (A) and H3K27me3 CUT&RUN signal around promoters of upregulated genes associated with binding motifs of YSE-relevant transcriptions (B) in the indicated LAD and non-LAD regions. (C) Genome browser view of ATAC-seq peaks and GATA4/6 binding motifs around the upregulated broad-lineage gene Cxcl12 , alongside tracks of bulk RNA-seq and H3K27me3 CUT&RUN from control and lamin-A/B1 DKO cells. An ATAC-seq peak containing GATA4/6 motifs is highlighted (dashed box). (D) Heatmap showing 3D chromatin interaction changes around Cxcl12 upon lamin-A/B1 loss. Boxed regions and arrows highlight increased interactions with transcriptionally active HiLands-R and reduced interactions with repressive HiLands-B. (E) Genome browser view of ATAC-seq and HNF4α binding motifs around the downregulated gene Afp with known functions in YSE cells, alongside tracks of bulk RNA-seq and H3K27ac CUT&RUN from control and lamin-A/B1 DKO cells. ATAC-seq peaks containing HNF4α motifs are highlighted (dashed box). (F) Heatmap showing 3D chromatin interaction changes around Afp upon lamin-A/B1 loss. Boxed regions and arrows indicate increased interactions with repressive HiLands-B. (G and H) Heatmaps of observed/expected (O/E) Hi-C interactions of the zoomed-in region around Afp outlined by the dashed box in (F) of control (G) and lamin-A/B1 DKO (H) YSE cells. The boxed region and arrows highlight reduced interactions between Afp and transcriptionally active HiLands-R upon lamin-A/B1 loss.

    Journal: bioRxiv

    Article Title: Lamins and lineage-relevant transcription factors coordinate gene expression in lineage development

    doi: 10.64898/2026.04.30.722071

    Figure Lengend Snippet: (A and B) Metaplots of H3K27ac CUT&RUN signal around promoters of downregulated genes associated with binding motifs of YSE-relevant transcription factors (A) and H3K27me3 CUT&RUN signal around promoters of upregulated genes associated with binding motifs of YSE-relevant transcriptions (B) in the indicated LAD and non-LAD regions. (C) Genome browser view of ATAC-seq peaks and GATA4/6 binding motifs around the upregulated broad-lineage gene Cxcl12 , alongside tracks of bulk RNA-seq and H3K27me3 CUT&RUN from control and lamin-A/B1 DKO cells. An ATAC-seq peak containing GATA4/6 motifs is highlighted (dashed box). (D) Heatmap showing 3D chromatin interaction changes around Cxcl12 upon lamin-A/B1 loss. Boxed regions and arrows highlight increased interactions with transcriptionally active HiLands-R and reduced interactions with repressive HiLands-B. (E) Genome browser view of ATAC-seq and HNF4α binding motifs around the downregulated gene Afp with known functions in YSE cells, alongside tracks of bulk RNA-seq and H3K27ac CUT&RUN from control and lamin-A/B1 DKO cells. ATAC-seq peaks containing HNF4α motifs are highlighted (dashed box). (F) Heatmap showing 3D chromatin interaction changes around Afp upon lamin-A/B1 loss. Boxed regions and arrows indicate increased interactions with repressive HiLands-B. (G and H) Heatmaps of observed/expected (O/E) Hi-C interactions of the zoomed-in region around Afp outlined by the dashed box in (F) of control (G) and lamin-A/B1 DKO (H) YSE cells. The boxed region and arrows highlight reduced interactions between Afp and transcriptionally active HiLands-R upon lamin-A/B1 loss.

    Article Snippet: The following antibodies were used for additional CUT&RUN: Lamin-A/C (Abcam, ab133256), Lamin-B1 (Abcam, ab16048), Lamin-B2 (Abcam, ab138516), H3K9me2 (Diagenode, C15200154), H3K9me3 (Active Motif, Cat. no. 39062), H3K27ac (Epicypher, 13–0059), H3K27me3 (Epicypher, 13-0055).

    Techniques: Binding Assay, RNA Sequencing, Control, Hi-C

    (A) Genome-wide matrix of topologically associated domains (TADs) shows that most interactions are intrachromosomal (diagonal intensity pattern indicates each chromosome plotted against itself). A unique interaction pattern between chromosomes 1p and 7q (black arrow) was observed in KT-47R1 but not in KT-47PT. (B) Hi-C identified an interchromosomal interaction between chromosome 1p32.3 ( GLIS1 locus) and chromosome 7q21 ( ABCB1 locus, black arrow) in KT-47R1. The light red vertical line marks the boundary between interacting regions of chromosomes 1 (right) and 7 (left). Red arcs indicate interactions between chromosomes 1 and 7 in KT-47R1, absent in KT-47PT (no blue arcs crossing the boundary). RNA-seq reads confirm upregulation of ABCB1 (black arrow) in KT-47R1. (C) CUT&Tag analysis shows H3K4me1 peaks within the interacting region of chromosome 1p32.3. Peaks are present in both KT-47PT and KT-47R1, but the chromatin interaction occurs only in KT-47R1. (D) FISH 1p32.3 break-apart analysis demonstrates no translocation involving 1p32.3 in KT-47PT, KT-47 pre-resistance, KT-47R1, or KT-47R2. Scale bars, 5 μm. (E) Chromosome 1 and 7 painting analysis indicated increased interaction (colocalization) between chromosomes 1 and 7 in KT-47R1 (48%) and KT-47R2 (48%) when compared to KT-47PT (19%) and KT-47PR (25%). Scale bars, 10 μm. n = 2 samples per group.

    Journal: Cell reports

    Article Title: Developmental reprogramming underlies chemotherapy resistance in favorable-histology Wilms tumor

    doi: 10.1016/j.celrep.2026.117063

    Figure Lengend Snippet: (A) Genome-wide matrix of topologically associated domains (TADs) shows that most interactions are intrachromosomal (diagonal intensity pattern indicates each chromosome plotted against itself). A unique interaction pattern between chromosomes 1p and 7q (black arrow) was observed in KT-47R1 but not in KT-47PT. (B) Hi-C identified an interchromosomal interaction between chromosome 1p32.3 ( GLIS1 locus) and chromosome 7q21 ( ABCB1 locus, black arrow) in KT-47R1. The light red vertical line marks the boundary between interacting regions of chromosomes 1 (right) and 7 (left). Red arcs indicate interactions between chromosomes 1 and 7 in KT-47R1, absent in KT-47PT (no blue arcs crossing the boundary). RNA-seq reads confirm upregulation of ABCB1 (black arrow) in KT-47R1. (C) CUT&Tag analysis shows H3K4me1 peaks within the interacting region of chromosome 1p32.3. Peaks are present in both KT-47PT and KT-47R1, but the chromatin interaction occurs only in KT-47R1. (D) FISH 1p32.3 break-apart analysis demonstrates no translocation involving 1p32.3 in KT-47PT, KT-47 pre-resistance, KT-47R1, or KT-47R2. Scale bars, 5 μm. (E) Chromosome 1 and 7 painting analysis indicated increased interaction (colocalization) between chromosomes 1 and 7 in KT-47R1 (48%) and KT-47R2 (48%) when compared to KT-47PT (19%) and KT-47PR (25%). Scale bars, 10 μm. n = 2 samples per group.

    Article Snippet: Antibodies included: IgG control (EpiCypher cat#13–0042), H3K27ac (EpiCypher cat#13–0059), H3K27me3 (EpiCypher cat#13–0055), H3K4me1 (EpiCypher cat#13–0057), H3K4me3 (Active Motif cat# 39159), H3K9me1 (Invitrogen cat# MA5-333-85), and H3K9me3 (Invitrogen cat#720093).

    Techniques: Genome Wide, Hi-C, RNA Sequencing, Translocation Assay