Figure 7

CHD1 and CHD2 control H3 and H3.3 occupancy at active regulatory regions. (A) Chromatin immunoprecipitation (ChIP-qPCR) analysis of control CHD1, CHD2 and double knockdown experiments at promoters associated with DNase hypersensitivity sites (DHS) show increased H3 occupancy with CHD1, CHD2 and double knockdowns in K562 cells. The strongest effect on H3 occupancy is observed with CHD2 knockdown. CHD2 knockdown also reduced H3.3 enrichment. (B) At intergenic and intragenic DNase sensitivity sites CHD1 and CHD2 knockdown increase H3 occupancy with the strongest trend observed in CHD2 and double knockdown cells. As for promoter sites, CHD2 knockdown reduced H3.3 enrichment. (C) Active tRNA loci-associated DNase sensitive sites show similar trends for both H3 and H3.3 occupancy. (D) Control loci from nonaccessible chromatin demonstrate the effects of CHD2 knockdown on H3 and H3.3 occupancy are specific to active regions. All data points represent mean values plotted from three biological replicates per loci tested. Differences compared to control were tested by one-way ANOVA, *P <0.05, **P <0.01, ***P <0.001.