Figure 1

CHD1 and CHD2 are recruited to active but not weak or inactive promoters in association with Pol II. (A) CHD1 and CHD2 occupancy is strongest in the active promoter chromatin state in K562 H1 embryonic stem cell (ESC) and GM12878 cells. CHD1 and CHD2 chromatin immunoprecipitation high throughput sequencing (ChIP-seq) data were normalized to input. Box plots illustrate the median and 25th to 75th percentile with whisker length determined by the Tukey method. In all cell types examined for both CHD1 and CHD2, enrichment at active promoters is statistically higher than at weak and inactive promoters (Kruskall-Wallis test with Dunn’s post test correction, k = 3, P <0.0001) (B) H3K4me2 and H3K4me3 are present at both active and weak promoters, while Pol II enrichment distinguishes the active and weak promoter chromatin state. (C) Examples of the transcription start site (TSS) of genes marked by H3K4me2/3 with differential Pol II, CHD1 and CHD2 binding. The GAL1K1 promoter - TSS1 is marked by H3K4me2/3 but is not bound by Pol II, CHD1 or CHD2, while the H3F3B promoter, TSS2, is strongly bound by Pol II along with CHD1 and CHD2. TSS3 of the UNK gene promoter displays H3K4me2/3 enrichment on a similar scale to the H3F3B gene but has weaker Pol II, CHD1 and CHD2 binding.