Histone deposition pathways determine the chromatin landscapes of H3.1 and H3.3 K27M oncohistones

Abstract

Lysine 27-to-methionine (K27M) mutations in the H3.1 or H3.3 histone genes are characteristic of pediatric diffuse midline gliomas (DMGs). These oncohistone mutations dominantly inhibit histone H3K27 trimethylation and silencing, but it is unknown if the oncohistone type affects gliomagenesis. We show that the genomic distributions of H3.1 and H3.3 oncohistones in human patient-derived DMG cells are consistent with the DNA replication-coupled deposition of histone H3.1 and the predominant replication-independent deposition of histone H3.3. Although H3K27 trimethylation is reduced for both oncohistone types, H3.3K27M-bearing cells retain some domains, and only H3.1K27M-bearing cells lack H3K27 trimethylation. Neither oncohistone interferes with PRC2 binding. Using Drosophila as a model, we demonstrate that inhibition of H3K27 trimethylation occurs only when H3K27M oncohistones are deposited into chromatin and only when expressed in cycling cells. We propose that oncohistones inhibit the H3K27 methyltransferase as chromatin patterns are being duplicated in proliferating cells, predisposing them to tumorigenesis.

Oncohistones: a roadmap to stalled development

“…All rights reserved in a DNA replication-coupled manner, while variant H3.3 histones are deposited in transcriptionally active genic and regulatory regions in a DNA replication-independent manner by distinct chaperones. These profiles reflect the deposition patterns of H3.1K27M versus H3.3K27M oncohistones [43,44].…”

The histone H3K9M mutation synergizes with H3K14 ubiquitylation to selectively sequester histone H3K9 methyltransferase Clr4 at heterochromatin

“…One of the key discrepancies regarding the methyltransferase sequestration model is in the case of H3.3K27M, in which most foci with high levels of H3.3K27M show little enrichment of the H3K27 methyltransferase PRC2 (Piunti et al, 2017). Although the reason for such a discrepancy is complex (Fang et al, 2018;Sarthy et al, 2020;Stafford et al, 2018), we speculate that additional mechanisms at defined genomic locations might change the kinetic properties of PRC2-H3.3K27M interactions, leading to sequestration of PRC2 at selective loci. Indeed, in H3.3K27M-expressing cells, PRC2 is sequestered at poised enhancers (Fang et al, 2018), and the H3.3K27M-PRC2 interactions can be modulated by the presence of H3K27me3 (Diehl et al, 2019;Stafford et al, 2018).…”

“…Introducing histones containing lysine-to-methionine mutations, such as H3K9M, H3K27M, and H3K36M, into mammalian or yeast cells all reduced methylation of their corresponding lysine residues on wild-type histones (Brumbaugh et al, 2019;Chan et al, 2013aChan et al, , 2013bFang et al, 2016;Herz et al, 2014;Lewis et al, 2013;Lu et al, 2016;Mohammad et al, 2017;Piunti et al, 2017;Sarthy et al, 2020;Shan et al, 2016;Stafford et al, 2018;Zhang et al, 2017), suggesting that they function in a dominant fashion and, possibly, through similar mechanisms. One of the most attractive models through which these mutations regulate global histone methylation is the sequestration of histone methyltransferases.…”

“…However, recent studies of the H3.3K27M mutation in vivo are not entirely consistent with the sequestration model. For example, chromatin immunoprecipitation sequencing (ChIP-seq) analyses of cancer cells expressing H3.3K27M found that, although the H3K27 methyltransferase PRC2 levels are higher at a set of poised enhancers that also contains H3.3K27M, most genomic loci containing high levels of H3.3K27M show no association with PRC2 (Fang et al, 2018;Piunti et al, 2017;Sarthy et al, 2020). Moreover, mass spectrometry analyses of proteins associated with H3.3K27M-containing nucleosomes did not detect higher levels of PRC2 than wild-type nucleosomes did (Herz et al, 2014).…”

Histone Variant H3.3 Mutations in Defining the Chromatin Function in Mammals

“…H3.3K27M is generally enriched in active chromatin, and H3.1K27M diffuses across the genome following H3.3 and H3.1 distribution, respectively. This variation appears to be associated with the different subtypes of pediatric glioma occurring by H3.3K27M and H3.1K27M [ 105 , 106 ]. Several studies have also pointed out that K27M mutation could affect H3K27ac levels, resulting in aberrant gene expression and enhancer dysfunction [ 100 , 107 ].…”