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(A) Venn diagrams showing the overlap of genomic regions co-occupied by Nanog and either mH2A1.1 (left) or mH2A1.2 (right) <t>in</t> <t>ESCs.</t> (B) Summary plots showing Nanog ChIP-seq signal (IP minus Input) across regions commonly co-bound by Nanog with either mH2A1.1 (left) or mH2A1.2 (right), centered on Nanog peaks and spanning ±2.5 kb. (C) Functional enrichment analysis (over-representation analysis, ORA) of genes near the Nanog/mH2A1.1 (left) and Nanog/mH2A1.2 (right) co-bound regions. Top 10 terms from the Wikipathways library are shown, ranked by adjusted p-value (P-Adjusted < 0.05). (D) Confocal images of ESCs treated with <t>retinoic</t> acid (lower panel) or untreated (upper panel), following lentiviral knockdown of mH2A1.1 (shRNA) or scramble control. Cells were fixed and stained with α-smooth muscle actin (α-SMA in green) to assess differentiation; nuclei counterstained with DAPI (in blue). Images acquired at 6days post-Retinoic Acid treatment. Scale bar: 40 μm. (E) Heatmaps depicting binding of Nanog (upper panel), Oct4 (middle panel), and Sox2 (bottom panel) to mH2A1.1 nucleosomes in ESCs, which are absent from MEFs, spanning ±2.5 kb from Nanog, Oct4 or Sox2 peak centers. (F) UpSet plot depicting overlapping regions between mH2A1.1 and Nanog, Oct4 or Sox2 and combinations thereof. The total number of mH2A1.1-nucleosome regions bound by any of the Oct4, Sox2 or Nanog is 25,117. The plot was created using Intervene. (G) Summary plots depicting the Averaged Signal (IP - Input) of Nanog (blue line) and mH2A1.1 (red line) in either Nanog exclusive regions (left panel), common mH2A1.1 and Nanog regions (middle panel) or common mH2A1.1-Nanog-Oct4-Sox2 regions (right panel). The horizontal gray dashed lines compare the peaks of Nanog signal among the three classes of regions. Common regions were defined by the UpSet plot (F) and were downsampled to acquire equal number of regions analyzed per region condition. (H) Same as (G) but for Oct4 binding (I) Same as (G) but for Sox2 binding
Retinoic Acid Ra, supplied by Santa Cruz Biotechnology, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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(A) Venn diagrams showing the overlap of genomic regions co-occupied by Nanog and either mH2A1.1 (left) or mH2A1.2 (right) <t>in</t> <t>ESCs.</t> (B) Summary plots showing Nanog ChIP-seq signal (IP minus Input) across regions commonly co-bound by Nanog with either mH2A1.1 (left) or mH2A1.2 (right), centered on Nanog peaks and spanning ±2.5 kb. (C) Functional enrichment analysis (over-representation analysis, ORA) of genes near the Nanog/mH2A1.1 (left) and Nanog/mH2A1.2 (right) co-bound regions. Top 10 terms from the Wikipathways library are shown, ranked by adjusted p-value (P-Adjusted < 0.05). (D) Confocal images of ESCs treated with <t>retinoic</t> acid (lower panel) or untreated (upper panel), following lentiviral knockdown of mH2A1.1 (shRNA) or scramble control. Cells were fixed and stained with α-smooth muscle actin (α-SMA in green) to assess differentiation; nuclei counterstained with DAPI (in blue). Images acquired at 6days post-Retinoic Acid treatment. Scale bar: 40 μm. (E) Heatmaps depicting binding of Nanog (upper panel), Oct4 (middle panel), and Sox2 (bottom panel) to mH2A1.1 nucleosomes in ESCs, which are absent from MEFs, spanning ±2.5 kb from Nanog, Oct4 or Sox2 peak centers. (F) UpSet plot depicting overlapping regions between mH2A1.1 and Nanog, Oct4 or Sox2 and combinations thereof. The total number of mH2A1.1-nucleosome regions bound by any of the Oct4, Sox2 or Nanog is 25,117. The plot was created using Intervene. (G) Summary plots depicting the Averaged Signal (IP - Input) of Nanog (blue line) and mH2A1.1 (red line) in either Nanog exclusive regions (left panel), common mH2A1.1 and Nanog regions (middle panel) or common mH2A1.1-Nanog-Oct4-Sox2 regions (right panel). The horizontal gray dashed lines compare the peaks of Nanog signal among the three classes of regions. Common regions were defined by the UpSet plot (F) and were downsampled to acquire equal number of regions analyzed per region condition. (H) Same as (G) but for Oct4 binding (I) Same as (G) but for Sox2 binding
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(A) Venn diagrams showing the overlap of genomic regions co-occupied by Nanog and either mH2A1.1 (left) or mH2A1.2 (right) <t>in</t> <t>ESCs.</t> (B) Summary plots showing Nanog ChIP-seq signal (IP minus Input) across regions commonly co-bound by Nanog with either mH2A1.1 (left) or mH2A1.2 (right), centered on Nanog peaks and spanning ±2.5 kb. (C) Functional enrichment analysis (over-representation analysis, ORA) of genes near the Nanog/mH2A1.1 (left) and Nanog/mH2A1.2 (right) co-bound regions. Top 10 terms from the Wikipathways library are shown, ranked by adjusted p-value (P-Adjusted < 0.05). (D) Confocal images of ESCs treated with <t>retinoic</t> acid (lower panel) or untreated (upper panel), following lentiviral knockdown of mH2A1.1 (shRNA) or scramble control. Cells were fixed and stained with α-smooth muscle actin (α-SMA in green) to assess differentiation; nuclei counterstained with DAPI (in blue). Images acquired at 6days post-Retinoic Acid treatment. Scale bar: 40 μm. (E) Heatmaps depicting binding of Nanog (upper panel), Oct4 (middle panel), and Sox2 (bottom panel) to mH2A1.1 nucleosomes in ESCs, which are absent from MEFs, spanning ±2.5 kb from Nanog, Oct4 or Sox2 peak centers. (F) UpSet plot depicting overlapping regions between mH2A1.1 and Nanog, Oct4 or Sox2 and combinations thereof. The total number of mH2A1.1-nucleosome regions bound by any of the Oct4, Sox2 or Nanog is 25,117. The plot was created using Intervene. (G) Summary plots depicting the Averaged Signal (IP - Input) of Nanog (blue line) and mH2A1.1 (red line) in either Nanog exclusive regions (left panel), common mH2A1.1 and Nanog regions (middle panel) or common mH2A1.1-Nanog-Oct4-Sox2 regions (right panel). The horizontal gray dashed lines compare the peaks of Nanog signal among the three classes of regions. Common regions were defined by the UpSet plot (F) and were downsampled to acquire equal number of regions analyzed per region condition. (H) Same as (G) but for Oct4 binding (I) Same as (G) but for Sox2 binding
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(A) Venn diagrams showing the overlap of genomic regions co-occupied by Nanog and either mH2A1.1 (left) or mH2A1.2 (right) <t>in</t> <t>ESCs.</t> (B) Summary plots showing Nanog ChIP-seq signal (IP minus Input) across regions commonly co-bound by Nanog with either mH2A1.1 (left) or mH2A1.2 (right), centered on Nanog peaks and spanning ±2.5 kb. (C) Functional enrichment analysis (over-representation analysis, ORA) of genes near the Nanog/mH2A1.1 (left) and Nanog/mH2A1.2 (right) co-bound regions. Top 10 terms from the Wikipathways library are shown, ranked by adjusted p-value (P-Adjusted < 0.05). (D) Confocal images of ESCs treated with <t>retinoic</t> acid (lower panel) or untreated (upper panel), following lentiviral knockdown of mH2A1.1 (shRNA) or scramble control. Cells were fixed and stained with α-smooth muscle actin (α-SMA in green) to assess differentiation; nuclei counterstained with DAPI (in blue). Images acquired at 6days post-Retinoic Acid treatment. Scale bar: 40 μm. (E) Heatmaps depicting binding of Nanog (upper panel), Oct4 (middle panel), and Sox2 (bottom panel) to mH2A1.1 nucleosomes in ESCs, which are absent from MEFs, spanning ±2.5 kb from Nanog, Oct4 or Sox2 peak centers. (F) UpSet plot depicting overlapping regions between mH2A1.1 and Nanog, Oct4 or Sox2 and combinations thereof. The total number of mH2A1.1-nucleosome regions bound by any of the Oct4, Sox2 or Nanog is 25,117. The plot was created using Intervene. (G) Summary plots depicting the Averaged Signal (IP - Input) of Nanog (blue line) and mH2A1.1 (red line) in either Nanog exclusive regions (left panel), common mH2A1.1 and Nanog regions (middle panel) or common mH2A1.1-Nanog-Oct4-Sox2 regions (right panel). The horizontal gray dashed lines compare the peaks of Nanog signal among the three classes of regions. Common regions were defined by the UpSet plot (F) and were downsampled to acquire equal number of regions analyzed per region condition. (H) Same as (G) but for Oct4 binding (I) Same as (G) but for Sox2 binding
Cis 9 Retinoic Acid 9cra, supplied by Millipore, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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9- cis-retinoic acid  (FUJIFILM)
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FUJIFILM 9- cis-retinoic acid
(A) Venn diagrams showing the overlap of genomic regions co-occupied by Nanog and either mH2A1.1 (left) or mH2A1.2 (right) <t>in</t> <t>ESCs.</t> (B) Summary plots showing Nanog ChIP-seq signal (IP minus Input) across regions commonly co-bound by Nanog with either mH2A1.1 (left) or mH2A1.2 (right), centered on Nanog peaks and spanning ±2.5 kb. (C) Functional enrichment analysis (over-representation analysis, ORA) of genes near the Nanog/mH2A1.1 (left) and Nanog/mH2A1.2 (right) co-bound regions. Top 10 terms from the Wikipathways library are shown, ranked by adjusted p-value (P-Adjusted < 0.05). (D) Confocal images of ESCs treated with <t>retinoic</t> acid (lower panel) or untreated (upper panel), following lentiviral knockdown of mH2A1.1 (shRNA) or scramble control. Cells were fixed and stained with α-smooth muscle actin (α-SMA in green) to assess differentiation; nuclei counterstained with DAPI (in blue). Images acquired at 6days post-Retinoic Acid treatment. Scale bar: 40 μm. (E) Heatmaps depicting binding of Nanog (upper panel), Oct4 (middle panel), and Sox2 (bottom panel) to mH2A1.1 nucleosomes in ESCs, which are absent from MEFs, spanning ±2.5 kb from Nanog, Oct4 or Sox2 peak centers. (F) UpSet plot depicting overlapping regions between mH2A1.1 and Nanog, Oct4 or Sox2 and combinations thereof. The total number of mH2A1.1-nucleosome regions bound by any of the Oct4, Sox2 or Nanog is 25,117. The plot was created using Intervene. (G) Summary plots depicting the Averaged Signal (IP - Input) of Nanog (blue line) and mH2A1.1 (red line) in either Nanog exclusive regions (left panel), common mH2A1.1 and Nanog regions (middle panel) or common mH2A1.1-Nanog-Oct4-Sox2 regions (right panel). The horizontal gray dashed lines compare the peaks of Nanog signal among the three classes of regions. Common regions were defined by the UpSet plot (F) and were downsampled to acquire equal number of regions analyzed per region condition. (H) Same as (G) but for Oct4 binding (I) Same as (G) but for Sox2 binding
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(A) Venn diagrams showing the overlap of genomic regions co-occupied by Nanog and either mH2A1.1 (left) or mH2A1.2 (right) in ESCs. (B) Summary plots showing Nanog ChIP-seq signal (IP minus Input) across regions commonly co-bound by Nanog with either mH2A1.1 (left) or mH2A1.2 (right), centered on Nanog peaks and spanning ±2.5 kb. (C) Functional enrichment analysis (over-representation analysis, ORA) of genes near the Nanog/mH2A1.1 (left) and Nanog/mH2A1.2 (right) co-bound regions. Top 10 terms from the Wikipathways library are shown, ranked by adjusted p-value (P-Adjusted < 0.05). (D) Confocal images of ESCs treated with retinoic acid (lower panel) or untreated (upper panel), following lentiviral knockdown of mH2A1.1 (shRNA) or scramble control. Cells were fixed and stained with α-smooth muscle actin (α-SMA in green) to assess differentiation; nuclei counterstained with DAPI (in blue). Images acquired at 6days post-Retinoic Acid treatment. Scale bar: 40 μm. (E) Heatmaps depicting binding of Nanog (upper panel), Oct4 (middle panel), and Sox2 (bottom panel) to mH2A1.1 nucleosomes in ESCs, which are absent from MEFs, spanning ±2.5 kb from Nanog, Oct4 or Sox2 peak centers. (F) UpSet plot depicting overlapping regions between mH2A1.1 and Nanog, Oct4 or Sox2 and combinations thereof. The total number of mH2A1.1-nucleosome regions bound by any of the Oct4, Sox2 or Nanog is 25,117. The plot was created using Intervene. (G) Summary plots depicting the Averaged Signal (IP - Input) of Nanog (blue line) and mH2A1.1 (red line) in either Nanog exclusive regions (left panel), common mH2A1.1 and Nanog regions (middle panel) or common mH2A1.1-Nanog-Oct4-Sox2 regions (right panel). The horizontal gray dashed lines compare the peaks of Nanog signal among the three classes of regions. Common regions were defined by the UpSet plot (F) and were downsampled to acquire equal number of regions analyzed per region condition. (H) Same as (G) but for Oct4 binding (I) Same as (G) but for Sox2 binding

Journal: bioRxiv

Article Title: Repurposed macroH2A Chromatin Landscapes Guide Cellular Reprogramming

doi: 10.64898/2025.12.11.693653

Figure Lengend Snippet: (A) Venn diagrams showing the overlap of genomic regions co-occupied by Nanog and either mH2A1.1 (left) or mH2A1.2 (right) in ESCs. (B) Summary plots showing Nanog ChIP-seq signal (IP minus Input) across regions commonly co-bound by Nanog with either mH2A1.1 (left) or mH2A1.2 (right), centered on Nanog peaks and spanning ±2.5 kb. (C) Functional enrichment analysis (over-representation analysis, ORA) of genes near the Nanog/mH2A1.1 (left) and Nanog/mH2A1.2 (right) co-bound regions. Top 10 terms from the Wikipathways library are shown, ranked by adjusted p-value (P-Adjusted < 0.05). (D) Confocal images of ESCs treated with retinoic acid (lower panel) or untreated (upper panel), following lentiviral knockdown of mH2A1.1 (shRNA) or scramble control. Cells were fixed and stained with α-smooth muscle actin (α-SMA in green) to assess differentiation; nuclei counterstained with DAPI (in blue). Images acquired at 6days post-Retinoic Acid treatment. Scale bar: 40 μm. (E) Heatmaps depicting binding of Nanog (upper panel), Oct4 (middle panel), and Sox2 (bottom panel) to mH2A1.1 nucleosomes in ESCs, which are absent from MEFs, spanning ±2.5 kb from Nanog, Oct4 or Sox2 peak centers. (F) UpSet plot depicting overlapping regions between mH2A1.1 and Nanog, Oct4 or Sox2 and combinations thereof. The total number of mH2A1.1-nucleosome regions bound by any of the Oct4, Sox2 or Nanog is 25,117. The plot was created using Intervene. (G) Summary plots depicting the Averaged Signal (IP - Input) of Nanog (blue line) and mH2A1.1 (red line) in either Nanog exclusive regions (left panel), common mH2A1.1 and Nanog regions (middle panel) or common mH2A1.1-Nanog-Oct4-Sox2 regions (right panel). The horizontal gray dashed lines compare the peaks of Nanog signal among the three classes of regions. Common regions were defined by the UpSet plot (F) and were downsampled to acquire equal number of regions analyzed per region condition. (H) Same as (G) but for Oct4 binding (I) Same as (G) but for Sox2 binding

Article Snippet: Differentiation of mouse ESCs was induced by retinoic acid (RA) (Santa-Cruz Biotechnology, sc-205589A), the main biologically active metabolite of vitamin A and one of the most important differentiation inducing factors ( Rohwedel et al , 1999 ).

Techniques: ChIP-sequencing, Functional Assay, Knockdown, shRNA, Control, Staining, Binding Assay