PRC2-binding regions are hotspots of DNA methylation entropy in pre-cancer and cancer

DNA methylation aberrations and variability are pervasive features of cancer, yet their relationship with chromatin regulation remains incompletely understood. Across hundreds of matched tumor–normal methylomes, regions with the highest methylation entropy in both tumor and normal tissues were consistently enriched for PRC2-associated factors. In tumors, inter-sample methylation variability was increased across the full range of PRC2-associated levels, while mean methylation progressively increased from low- to high-PRC2-binding regions; this gradient was substantially weaker in matched normal tissues. PRC2-associated regions with higher DNA methylation levels were preferentially associated with poised and repressed chromatin states, reduced chromatin accessibility, and reduced gene expression. Independent normal–precancer–cancer cohorts showed that this PRC2-associated methylation state emerges early, with precancerous and malignant tissues displaying highly similar profiles that are distinct from those of healthy tissues. Single-cell colon cancer methylomes independently confirmed increased methylation entropy at PRC2 regions. Higher PRC2-region entropy was associated with scores reflecting hypoxic states, aggressive tumor features, and poorer survival outcomes. Collectively, these findings identify PRC2-binding regions as hotspots of DNA methylation variability that become dysregulated during tumorigenesis.