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

Abstract

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.