Distinct roles for canonical and variant histone H3 lysine 36 in Polycomb silencing

Abstract

Polycomb complexes regulate cell-type specific gene expression programs through heritable silencing of target genes. Trimethylation of histone H3 lysine 27 (H3K27me3) is essential for this process. Perturbation of H3K36 is thought to interfere with H3K27me3. We show that mutants of Drosophila replication-dependent (H3.2K36R) or -independent (H3.3K36R) histone H3 genes generally maintain Polycomb silencing and reach later stages of development. In contrast, combined (H3.3K36RH3.2K36R) mutants display widespread Hox gene misexpression and fail to develop past the first larval stage. Chromatin profiling revealed that the H3.2K36R mutation disrupts H3K27me3 levels broadly throughout silenced domains, whereas these regions are mostly unaffected in H3.3K36R animals. Analysis of H3.3 distributions showed that this histone is enriched at presumptive PREs (Polycomb Response Elements) located outside of silenced domains but relatively depleted from those inside. We conclude that H3.2 and H3.3 K36 residues collaborate to repress Hox genes using different mechanisms.

Set2 and H3K36 regulate theDrosophilamale X chromosome in a context-specific manner, independent from MSL complex spreading

“…As shown in Fig. 1B, addition of an HWT transgene fully rescued the larval and pupal viability defects seen in K36R -only animals [51]. However, there was no significant change in the number of males that eclose from a K36R/HWT cross compared to HWT/HWT controls (Fig.…”

“…Note that Set2 null and 12x H3.2 K36R animals fail to eclose as adults, but wandering L3 males from these lines are readily obtained [37, 53]. To ascertain whether H3.2 K36 and H4 K16 residues interact genetically, we carried out complementation analysis between multi-gene families [51]. That is, we combined two 12x histone constructs in trans, and assayed pupation and eclosion frequencies of the resulting progeny.…”

“…A significant change in viability by comparison to control crosses would suggest that the two residues cooperate in common pathways. Previously, we found that H3.2 K36R interacted strongly with K27R but was fully complemented by a K9R mutation [51].…”

Drosophila melanogasterSet8 and L(3)mbt function in gene expression independently of histone H4 lysine 20 methylation

“…CUT&RUN 20 third instar larval wing discs per replicate were dissected and processed as previously described (Uyehara et al 2022) with rabbit α-GFP (1:100, Rockland 600-401-215) or mouse α-H4K20me1 (1:100, ThermoFisher MA5-18067) and pAG-MNase (1:100, UNC core, (Salzler et al 2023)).…”

Histone H3 E50K mutation confers oncogenic activity and supports an EMT phenotype

“…A challenge with understanding how the amino acid changes that occur in oncohistones alter histone function in the context of chromatin is that histones genes are present in multiple copies, creating a situation where a single oncohistone protein is present in the background of wildtype histones. One approach that has been utilized to understand how specific amino acid changes alter histone function in the context of chromatin has been to employ model systems (27)(28)(29)(30). This approach benefits from the fact that the histone proteins are some of the most evolutionarily conserved proteins (31) and the fact that simple model systems such as yeast have far fewer copies of histone genes than higher eukaryotes.…”