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 how 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.

The H3.3K27M oncohistone antagonizes reprogramming in Drosophila

“…We next looked at the effect of the H3.3K27M oncohistone on H3K27me3 patterns in the eye. The oncohistone is incorporated into chromatin by histone H3.3-specific chaperones at active promoters and enhancers, and at lower levels by DNA replication throughout the genome [Chan et al, 2013; Piunti et al, 2017; Mohammad et al, 2017; Sarthy et al, 2020], and expression of H3.3K27M in eye discs gives a similar promoter enrichment with background throughout the genome when profiled using an antibody to the K27M epitope (Supplementary Figure 1E). Expression of the oncohistone reduces H3K27me3 staining (Figure 2G,I), and quantitative chromatin profiling of glioma cell lines has previously shown that H3K27me3 is globally reduced but a few domains remain [Sarthy et al, 2020].…”

“…The oncohistone is incorporated into chromatin by histone H3.3-specific chaperones at active promoters and enhancers, and at lower levels by DNA replication throughout the genome [Chan et al, 2013; Piunti et al, 2017; Mohammad et al, 2017; Sarthy et al, 2020], and expression of H3.3K27M in eye discs gives a similar promoter enrichment with background throughout the genome when profiled using an antibody to the K27M epitope (Supplementary Figure 1E). Expression of the oncohistone reduces H3K27me3 staining (Figure 2G,I), and quantitative chromatin profiling of glioma cell lines has previously shown that H3K27me3 is globally reduced but a few domains remain [Sarthy et al, 2020]. By profiling eye portions of imaginal discs with oncohistone expression, we find that H3K27me3 still coats domains, although with more dispersion between domains that we attribute to the lower H3K27me3 signal in oncohistone-expressing cells (Figure 5C).…”

Histone Variants: Guardians of Genome Integrity

“…Specific antibodies have been raised against several of these mutations, serving as powerful tools to refine cancer diagnosis. Importantly, the H3.1 and H3.3 point mutations do not affect residues involved in histone chaperone binding and thus do not alter the deposition patterns of these oncohistones into chromatin as shown for the K27M mutation [129,130]. These mutations localize to the N-terminal tails of histones, at or in the vicinity of modifiable residues and affect histone PTMs (methylation and acetylation) through various mechanisms.…”

“…Noteworthy, even though H3.1 and H3.3 variants can bear identical amino acid substitutions in cancer, there are significant differences between these mutated histone variants. For instance, H3.1K27M and H3.3K27M are differentially distributed in chromatin and H3.1K27M results in stronger reduction of H3K27me3 levels [130]. H3.1K27M and H3.3K27M also promote distinct oncogenic transcriptional programs in diffuse intrinsic pontine gliomas (DIPGs) [120,154] involving variant-specific patterns of active enhancers [143].…”

Histone variants at a glance

“…ATRX and DAXX deposit H3.3 in telomeres, imprinted genes and other heterochromatic loci, where it is modified with the trimethlyated lysine 9 heterochromatic mark (denoted H3K9me3) to maintain heterochromatin at these locations ( Drane et al, 2010 ; Elsässer et al, 2015 ; Goldberg et al, 2010 ; Voon et al, 2015 ; Wong et al, 2010 ). The difference between deposition pathways for RC H3.1 and RI H3.3 underlies the more-severe effects of pediatric diffuse midline gliomas caused by H3.1K27M mutations than those caused by H3.3K27M mutations, both of which inhibit global formation of H3K7me3, which normally prevents tumorigenesis ( Sarthy et al, 2020 ).…”