Fig. 3 | Nature Communications

Fig. 3

From: A non-canonical BRD9-containing BAF chromatin remodeling complex regulates naive pluripotency in mouse embryonic stem cells

Fig. 3

GBAF and esBAF localize to distinct genomic elements. a Venn diagram overlap of BRG1, BRD9, and ARID1A ChIP sites, with n representing the number of observed peaks. b Heat map of BRD9 and BRG1 ChIP signal ± 3 kilobases (kb) centered on the BRD9 peak, ranked according to BRD9 read density. c Significance of binding overlap between BRD9, BRG1, and ARID1A ChIP sites. The natural log of p values were calculated using hypergeometric distribution (mergePeaks.pl in HOMER). d Co-occurrence analysis showing the natural log of the ratio of the observed number of overlapping peaks over the expected values. This was done for BRD9, BRG1, and ARID1A ChIP sites against publicly available ChIP-Seq data for the histone modifications H3K4me, H3K4me3, H3K27me3, and H3K27ac. Poised enhancers are defined by sites that contain H3K4me1 but lack H3K27ac, whereas active enhancers are sites that are positive for both modifications. Super enhancers are H3K4me+, H3K27ac+, and Med1-high sites. e ChIP-Seq signal of BRG1, BRD9, and ARID1A ± 2 kb surrounding BRG1 peak center at promoters and distal sites. f ChIP-Seq signal of BRG1, BRD9, and ARID1A ± 50% size of a topologically associating domain (TAD) around a TAD