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Fig. 2 | BMC Biology

Fig. 2

From: ARID1A-dependent maintenance of H3.3 is required for repressive CHD4-ZMYND8 chromatin interactions at super-enhancers

Fig. 2

Genome-wide analysis of ARID1A-dependent H3.3. A MA plot of shARID1A vs. control differential H3.3 ChIP-seq (n = 2), across 67,502 tested genomic regions. Regions are colored based on shARID1A differential H3.3 significance. Inset pie chart depicts distribution of significantly increasing and decreasing H3.3 regions (csaw/edgeR FDR < 0.05) compared to stable H3.3 (FDR > 0.05). FDR < 0.05 was used as the significance threshold for all downstream analyses. B shARID1A differential H3.3 regions segregated by detection of ARID1A binding in wild-type cells. Left, MA plot with all genome-wide H3.3 tested regions, colored by ARID1A binding status. Right, box plot quantification of shARID1A log2FC H3.3 abundance, segregated by ARID1A binding status. Statistic is two-tailed, unpaired Wilcoxon’s test. C Analysis of canonical H3 (H3.1/3.2) changes (ChIP-seq, n = 2) at H3.3-marked genomic regions following ARID1A knockdown (shARID1A), segregated by ARID1A binding status as in B. Statistic is two-tailed, unpaired Wilcoxon’s test. D Enrichment of ARID1A binding detection at regions with decreasing H3.3 following ARID1A loss compared to all tested H3.3 regions. Statistics are hypergeometric enrichment test and pairwise two-tailed Fisher’s exact test. E Magnitude of H3.3 change (log2FC) among ARID1A-bound, shARID1A significantly decreasing vs. increasing H3.3 regions. Statistic is two-tailed, unpaired Wilcoxon’s test. F Distribution of H3.3-enriched region widths among shARID1A stable vs. increasing vs. decreasing H3.3 regions. Statistic is two-tailed, unpaired Wilcoxon’s test. G Chromatin state enrichment among shARID1A increasing and decreasing H3.3 regions, calculated per 200 bp genomic interval. Statistic is hypergeometric enrichment. H Top 10 significant (FDR < 0.05) enriched Hallmark pathways (left) and GO Biological Process gene sets (right) among genes with ARID1A-bound, shARID1A decreasing promoter-proximal H3.3. I Representative hg38 locus near CCL2 displaying H3.3 maintained by ARID1A chromatin interactions. *** p < 0.001

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