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. 2024 Oct 17;84(20):3899-3915.e7.
doi: 10.1016/j.molcel.2024.09.015. Epub 2024 Oct 4.

The H3.3K36M oncohistone disrupts the establishment of epigenetic memory through loss of DNA methylation

Joydeb Sinha  1 , Jan F Nickels  2 , Abby R Thurm  3 , Connor H Ludwig  4 , Bella N Archibald  4 , Michaela M Hinks  4 , Jun Wan  4 , Dong Fang  5 , Lacramioara Bintu  6
Affiliations

The H3.3K36M oncohistone disrupts the establishment of epigenetic memory through loss of DNA methylation

Joydeb Sinha et al. Mol Cell. .

Abstract

Histone H3.3 is frequently mutated in tumors, with the lysine 36 to methionine mutation (K36M) being a hallmark of chondroblastomas. While it is known that H3.3K36M changes the epigenetic landscape, its effects on gene expression dynamics remain unclear. Here, we use a synthetic reporter to measure the effects of H3.3K36M on silencing and epigenetic memory after recruitment of the ZNF10 Krüppel-associated box (KRAB) domain, part of the largest class of human repressors and associated with H3K9me3 deposition. We find that H3.3K36M, which decreases H3K36 methylation and increases histone acetylation, leads to a decrease in epigenetic memory and promoter methylation weeks after KRAB release. We propose a model for establishment and maintenance of epigenetic memory, where the H3K36 methylation pathway is necessary to maintain histone deacetylation and convert H3K9me3 domains into DNA methylation for stable epigenetic memory. Our quantitative model can inform oncogenic mechanisms and guide development of epigenetic editing tools.

Keywords: DNA methylation; H3.3K36M; H3K36me2; H3K36me3; KRAB; NSD1; SETD2; epigenetic memory; heterochromatin; oncohistone.

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Conflict of interest statement

Declaration of interests L.B. is a co-founder of Stylus Medicine and a member of its scientific advisory board.

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