Figure 4

CHD1 and CHD2 co-occupy active promoters but show different binding profiles across the transcription start site (TSS). (A) Statistically significant high confidence peaks from CHD1 and CHD2 chromatin immunoprecipitation sequencing (ChIP-seq) data were intersected with chromatin state annotations from K562 cells using model-based analysis for ChIP-seq (MACS) with a stringent cut-off p value of 1 x 10^-15. The majority of CHD1 (94%) and CHD2 (78%) binding sites fall within an active promoter or enhancer chromatin state or both as defined by Ernst et al. (B) The majority of CHD1 and CHD2 bound sites are overlapping; 60% of the 7,736 CHD2 binding sites overlap with at least one of 9,827 CHD1 peaks. (C) At highly expressed genes defined in the top 20% expression quintile, CHD1 binding profile follows the enrichment of H3k4me2/3-marked nucleosomes. In contrast, CHD2 binds strongest across the micrococcal nuclease (MNase) sensitive nucleosome depleted region (NDR) at the TSS.