Fig. 2: MacroH2A regulates enhancer activity.

a Expression levels at the CRE grouped by the five classes in human mammary epithelial cells (HMEC), normal human melanocytes (NHM), the breast cancer cell line (MCF7) and the human hepatocellular carcinoma cell line (HepG2) quantified by RNA-seq data from ENCODE reference epigenome for HMEC (total), MCF7 (poly-A) and HepG2 (total), and from Fontanals-Cirera et al.⁷³ for NHM (total). The number of datapoints, n, equals the number of CRE per class shown in Fig. 1c. b Expression levels by RNA-seq from normal breast samples (averaged across 113 samples) from TCGA³⁵ at enhancers that overlap the annotated CRE in HMEC. The number of datapoints, n, is shown below each box. c Expression levels by RNA-seq from Roadmap reference epigenome (E119) at protein-coding genes directly associated with the CRE from HMEC (associations obtained from GeneHancer) and super-enhancers (annotated using LILY). Inactive only, mBE only and ATAC only: genes associated with only Inactive, mBE or ATAC only classes of CRE respectively; Active Comb: genes associated with at least one Active CRE and possibly other combination of CRE classes; Comb: genes associated with all other combinations of CRE classes; SE: genes associated with those CRE identified as super-enhancers. The number of datapoints, n, is shown below each box. The expression data is represented as boxplots where the middle line represents the median, the lower and upper edges of the rectangle represent the first and third quartiles and the lower and upper whiskers represent the interquartile range (IQR) × 1.5. Outliers beyond the end of the whiskers are plotted individually. d Upset plots showing the intersection of mBE and APL (Active Promoter-Like) CRE loci between the four cell lines. e Top 5 most significant KEGG pathways sorted by Benjamini-Hochberg adjusted p-value of the minimum hypergeometric (mHG) test performed by Cistrome-GO on genes associated with mBE and APL (Active Promoter-Like) common in HMEC and MCF7.