Extended Data Fig. 7: Clonal methylation at functional regions is association with epithelial transcriptional output in HCT116.

a, Example for selection of clones for KNN-based normalization of DNA methylation over the clonal HCG (y axis) and LCG (x axis) space. Red dots indicate the K = 25 nearest neighboring clones used to normalize methylation of the selected clone (shown as blue dot). b, Distribution of correlations between average methylation of capture regions in clones to average methylation of clones in Low-CG (LCG) loci before (grey) and after (black) KNN normalization. c, same as b for High-CG (HCG) loci. d, Clustering of Spearman’s cross-correlation between gene expression and normalized average methylation of capture regions over 251 HCT116 clones covered simultaneously by RNA-seq and PBAT-capture. Green annotation of genes indicates epithelial genes. e, Epithelial transcriptional output per clone (x-axis) and clonal average methylation (y-axis) in 73 capture regions defined in d as Epithelial regions (Ep. regions, top) and 62 capture regions defined in d as EMT related regions (bottom) in 155 HCT116 clones, covered by at least 50 K UMIs and 50 K on-target methylation calls. f, As in e, showing expression of EMT related gene Zinc finger E-box-binding homeobox 1 (ZEB1) and methylation in Epithelial (top) and EMT (bottom) associated capture regions defined in d. g, Pooled average methylation of enhancer CpGs in EpCAM-high and -low clones, highlighting enhancers of epithelial up- (blue) or down-regulated (red) genes.