Skip to main content
Fig. 4 | BMC Biology

Fig. 4

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

Fig. 4

Characterization of ARID1A, CHD4, and ZMYND8 chromatin interactions co-regulating H3.3. A Genome-wide associations between ARID1A binding at H3.3+ vs. H3.3− regions for all 1135 transcriptional regulator peak sets included in the ReMap2020 peak database. Labeled factors exhibit an H3.3+ ARID1A binding association with genomic odds ratio >2 and overlap with >0.1% of ARID1A binding sites. ZMYND11 and ZMYND8 (bolded) are two of the top factors most associated with H3.3+ ARID1A binding. B Chromatin model schematic depicting hypothesized relationship between ARID1A-SWI/SNF and ZMYND8 co-regulation of H3.3, possibly mediated by co-factors. C ARID1A co-immunoprecipitation detecting physical interaction with NuRD catalytic subunit CHD4, but not ZMYND8. D CHD4 co-immunoprecipitation detecting physical interactions with both ARID1A and ZMYND8. E 10–30% glycerol gradient sedimentation and immunoblotting for SWI/SNF, NuRD, and ZMYND8. Relative fractions display native protein complexes transitioning from low molecular weight (left) to high molecular weight (right). Underlined fractions highlight potential interacting native complexes containing ZMYND8 and members of SWI/SNF (BAF) and NuRD (Mi-2β). F Genome-wide ChIP-seq (n = 2) peak overlaps between ARID1A, CHD4, ZMYND8, and H3.3. Peak numbers within the Euler diagram are approximations and not mutually exclusive due to varying peak sizes. G Example locus on chromosome 10 displaying ARID1A, CHD4, ZMYND8, and H3.3 co-regulation. H Enrichment for ARID1A co-regulation of H3.3 peaks bound by CHD4 and/or ZMYND8. Statistic is two-tailed Fisher’s exact test. I Average ChIP-seq signal density histograms for ARID1A (left) and H3.3 (right) at H3.3 peaks bound by CHD4 and/or ZMYND8. J H3.3 abundance (ChIP FPKM) at ARID1A-bound shARID1A differential H3.3 regions co-bound by CHD4 or ZMYND8. Statistic is two-tailed, unpaired Wilcoxon’s test. K Positive association between CHD4 binding (top) and negative association between ZMYND8 binding (bottom) and ARID1A maintenance of H3.3 chromatin, genome-wide. Statistic is two-tailed Fisher’s exact test. L Average ChIP-seq signal density histograms for ARID1A, H3.3, CHD4, and ZMYND8 across ARID1A-bound H3.3 regions that decreased or were stable with shARID1A

Back to article page