RNA polymerase II (Pol II)–bound genes respond opposite to that of PRC2-bound genes upon perturbation of SWI/SNF or NuRD activities. (A) The composition of the SWI/SNF and NuRD remodeling complexes. BRG1 (SWI/SNF) and CHD4 (NuRD) are the ATPase subunits of these complexes. SWI/SNF supports open whereas NuRD supports closed chromatin states at gene promoters. Also shown are the SWI/SNF and NuRD target genes in mESCs (N = 9345) binned into groups of 25 each and rank-ordered based on the Pol II binding levels at their promoters. For each bin, the median gene expression fold changes following Chd4 or Brg1 knockdown (KD) are shown. (B) Changes in promoter accessibility at genes that are up-regulated, neutral, or down-regulated following KD of Brg1 (left) or Chd4 (right). Standard error is represented by a shaded area around the lines. (C) BRG1 and CHD4 binding signals at the promoter of genes that are up-regulated, neutral, or down-regulated following KD of Brg1 (left) or Chd4 (right). (D) Occupancy levels of CHD4, BRG1, Pol II, EZH2, and histone modifications (H3K27ac and H3K27me3) at active (N = 7166) and bivalent (N = 2179) gene promoters. Active promoters are further subclassified based on their widths: narrow, ≤500 bp; medium, 500–1000 bp; broad, >1000 bp. Genes are binned into groups of 25 each and rank-ordered based on the Pol II binding levels at their promoters. For each bin, the median gene expression fold changes following Chd4 or Brg1 KD or during MEF-to-mESC reprogramming. Also shown are the changes in absolute (spike-in normalized) nascent RNA levels upon BRG1 inhibitor treatment (BRM014 for 3 h) and Chd4 KD. Genes corresponding to the KEGG pathways regulated by high/average Pol II–bound and low Pol II–bound/bivalent genes are marked on the heatmap (Supplemental Fig. S3A).
