Replicative history as a major determinant of epigenetic noise across human tissues

Abstract

DNA methylation changes accumulate with age through both regulated and stochastic processes, yet the determinants of epigenetic information loss remain poorly defined. Using genome-wide DNA methylation profiles from 1,531 healthy human samples spanning 14 tissues, we quantified epigenetic noise by Shannon entropy and corrected it for cellular and tissue heterogeneity. Adjusted entropy was consistently low in promoters, first exons and CpG islands, and high in CpG-poor and intergenic regions. Cumulative mitotic history showed a stronger association with epigenetic noise than chronological age, explaining most of its variance particularly within CpG-rich regulatory regions. By contrast, age-related, replication-independent effects predominated outside CpG islands and in low-proliferative tissues such as the brain. Moreover, biological age acceleration was largely attributable to cell division in a tissue-specific manner. Collectively, mitotic history emerges as a major determinant of epigenetic noise accumulation across human tissues, while genomic context modulates regional vulnerability to methylation information loss during aging.