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Fig. 3 | BMC Biology

Fig. 3

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

Fig. 3

Transcriptional effects of H3.3 depletion and overlap with ARID1A. A Baseline relative linear expression of H3F3A (H3-3A) and H3F3B (H3-3B) gene isoforms encoding H3.3, as measured by RNA-seq (n = 3). B Western blot for H3.3 and total H3 in control vs. siH3F3B treated cells. C Global transcriptomic effects of 24,192 genes following H3.3 knockdown via siH3F3B treatment (RNA-seq, n = 3). Red dots represent significant DE genes (DESeq2, FDR < 0.001). D Relative linear expression of H3F3A and H3F3B by RNA-seq in control and siH3F3B cells (n = 3). E Volcano plot depicting siH3F3B vs. control differential gene expression (DGE). Top significant genes are labeled. F Significant overlap in DE genes following H3.3 knockdown (siH3F3B) vs. ARID1A knockdown (siARID1A). Statistic is hypergeometric enrichment. G Directional segregation of siH3F3B/siARID1A overlapping DE genes. A positive association is observed by chi-squared test, i.e., genes are more likely to be upregulated or downregulated in both conditions as opposed to antagonistic regulation. H Scatter plot of siH3F3B vs. siARID1A expression log2FC (with shrinkage correction) for all 19,900 transcriptome-wide commonly detected genes. Statistics are Pearson (r) and Spearman (rs) correlation coefficients. Colored dots indicate significant DE genes (FDR < 0.001) in both treatment conditions. I Association between H3.3 transcriptional repression (siH3F3B upregulation) and transcriptional co-regulation by ARID1A (siARID1A DE). Statistic is two-tailed Fisher’s exact test. J Scatter plot of 196 shared DE genes upregulated following knockdown of either H3.3 or ARID1A. These genes are mutually repressed by H3.3 and ARID1A. K Top significant (FDR < 0.05) enriched gene sets among the 196 ARID1A-H3.3 mutually repressed genes among various gene set databases

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