BAF250a-dependent Brg1 enrichment in early to late (EtoL) switching domains. (A) Genome-wide relationship between Brg1 enrichment and replication timing. The x-axis shows the embryonic stem cell (ESC) replication timing data averaged in 200-Kb windows and the y-axis shows the number of Brg1 binding sites in each corresponding window. The smoothed blue line in the plot shows the average number of Brg1 sites per 200-Kb segment (thicker gray line shows the standard error). (B) Average number of Brg1 binding sites per 200-Kb segment that switched EtoL or LtoE after loss of Brg1 (FDR = 1% and 5% segments from Figure 3D) and comparison to the remainder of the genome (‘non-switching’). Based on this data, 400 to 800 Kb EtoL switching domains are thought to have 3.5 to 7.0 Brg1 binding sites. (C) BAF250a-dependent Brg1 enrichment within the EtoL domain (chr4: 104.5 to 105.0 Mb and chr7: 82.5 to 83.0 Mb from Figure 3F), revealed by Brg1 chromatin immunoprecipitation (Brg1-ChIP). Brg1 enrichment was analyzed at multiple sites within the chr4 domain (site-1: 104654835 to 104654965, site-2: 104668986 to 104669071, site-3: 104693231 to 104693309, site-4: 104713676 to 104713776) and chr7 domain (site-1: 82610306 to 82610419, site-2: 82647473 to 82647844, site-3: 82660145 to 82660243, site-4: 82662755 to 82662863) both in mock-treated (blue) and 4-hydroxytamoxifen (OHT)-treated (red) BAF250a flox/flox ESCs. These are Brg1 binding sites identified by ChIP-seq  and their positions relative to EtoL domains are shown under the Brg1-ChIP result. The binding of Brg1 at Oct4 and Nkx2.5 promoters was used as positive and negative controls, respectively. The Oct4 promoter region also showed a BAF250a-dependent Brg1 binding. *P <0.05; nsP >0.05 (no significant difference). Statistical analysis was performed by a two-tailed Student’s t-test.