Fig. 4

Group 1 chromatin remodellers highly overlap accessible DNA regions. a The ChIP-seq signal of the chromatin remodellers and the signal from the ENCODE DNAseI peaks were determined at DNAseI called sites, and then Pearson’s correlation scores were calculated between each data set and compiled into a matrix. The matrix was ordered by hierarchical clustering using the distance between correlation scores. This resulted in the Group 1 remodellers clustering with the DNAseI data and Group 2 remodellers clustering separately. Samples are presented in the same order on both the x- and y-axis. b Enrichment of chromatin remodeller binding sites at DNAse1 sites. Significant enrichment is defined as a score above one and significantly depleted as below one with Benjamini–Hochberg adj p-value, ***p < 0.001 or **p < 0.05. c Nucleosome occupancy defined from NOMe-seq ± 2 kb from the centre of chromatin remodeller binding sites. d Boxplot of the relationship between gene expression (TPM) and remodeller binding at promoters of genes that are expressed in LNCaP cells. Expressed genes were divided into genes that have a higher enrichment of Group 1 remodellers (green) at their promoter and those that have a higher enrichment of Group 2 remodellers (purple) at their promoter. The expression of Group 1 is significantly higher (p < 0.001, Wilcox rank sum, one-tailed) than Group 2. e Enrichment scores of the top 10 GO terms for promoters with a higher signal of Group 1 remodellers (Green) or a higher signal of Group 2 remodellers (purple)