PRC2-binding regions are hotspots of DNA methylation entropy in pre-cancer and cancer
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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.
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BibTeX
@misc{bukovec2026prc2binding,
title = {{PRC2-binding regions are hotspots of DNA methylation entropy in pre-cancer and cancer}},
author = {D. Bukovec and M. S. Misheva and M. Gjorgjievska and G. Kungulovski},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.11.758285},
url = {https://www.biorxiv.org/content/10.64898/2026.10.11.758285v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - PRC2-binding regions are hotspots of DNA methylation entropy in pre-cancer and cancer
AU - D. Bukovec
AU - M. S. Misheva
AU - M. Gjorgjievska
AU - G. Kungulovski
PY - 2026
DA - 2026/10/11
PB - bioRxiv
DO - 10.64898/2026.10.11.758285
UR - https://www.biorxiv.org/content/10.64898/2026.10.11.758285v1
AB - 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.
ER -