Understanding the language of Lys36 methylation at histone H3

Abstract

Histone side chains are post-translationally modified at multiple sites, including at Lys36 on histone H3 (H3K36). Several enzymes from yeast and humans, including the methyltransferases SET domain-containing 2 (Set2) and nuclear receptor SET domain-containing 1 (NSD1), respectively, alter the methylation status of H3K36, and significant progress has been made in understanding how they affect chromatin structure and function. Although H3K36 methylation is most commonly associated with the transcription of active euchromatin, it has also been implicated in diverse processes, including alternative splicing, dosage compensation and transcriptional repression, as well as DNA repair and recombination. Disrupted placement of methylated H3K36 within the chromatin landscape can lead to a range of human diseases, underscoring the importance of this modification.

Figure 1. Domain structures of enzymes that methylate H3K36

a | A schematic of the enzymes that have been shown to promote the formation of methylated Lys36 on histone H3 (H3K36). With the exception of fly maternal-effect sterile 4 (MES-4), only human enzymes are shown. The SET domain is shown with its pre (AWS) and post domains; C5HCH is a zinc-finger (ZNF) domain; WW domains are known to interact with Pro-rich peptides; the PWWP domain is known to interact with trimethylated H3K36; and the AT hook is a DNA-binding domain. All domain assignments were derived from Ensembl. b | Depiction of the transitions between the multiple H3K36 methylation states, highlighting the enzymes that have been shown to function in changing a given methylation state. ASH1L, ASH1-like; BAH, bromo- associated homology; BROM, bromodomain; HMG, high mobility group; MYND, myeloid, Nervy and DEAF-1 ZNF; NIDs, nuclear receptor interaction domains; NSD, nuclear receptor SET domain-containing; PHD, plant homeodomain; RuBisCo, ribulose-1,5-bisphosphate carboxylase oxygenase; SETD, SET domain-containing; SETMAR, SET domain and mariner transposase fusion gene-containing; SMYD2, SET and MYND domain-containing 2.

Figure 2. H3K36me3-dependent prevention of aberrant transcription in yeast

Actively transcribing RNA polymerase II (RNAPII) displaces acetylated nucleosomes. These evicted histones are reincorporated into nucleosomes and chromatin behind the polymerase. As SET domain-containing 2 (Set2) binds RNAPII, this promotes the trimethylation of Lys36 on histone H3 (H3K36me3) in the newly incorporated nucleosomes. H3K36me3 serves as a ‘mark’ that the reduced potassium dependency 3 (Rpd3) deacetylase complex binds; this complex facilitates local nucleosome deacetylation, preventing aberrant, spurious transcription in the wake of RNAPII progression through a region. CTD, carboxy-terminal domain; HAT, histone acetylase; m⁷G, 7-methylguanosine.

Figure 3. H3K36me3 influences alternative splicing in a cell-type specific manner

The fibroblast growth factor receptor 2 (FGFR2) locus that undergoes alternative splicing consists of two mutually exclusive exons, IIIb and IIIc, which are located between the constitutive exons 7 and 10. Mesenchymal stem cells favour the inclusion of exon IIIc and achieve this by repressing splicing of exon IIIb. Nucleosomes present near exon IIIb contain the SET domain-containing 2 (SETD2)-dependent trimethylated Lys36 on histone H3 (H3K36me3) ‘mark’ and its reader protein MORF-related gene 15 (MRG15). MRG15 also interacts with polypyrimidine tract-binding protein (PTB), a known repressor of exon inclusion, and this may be the mechanism by which the methylated H3K36 mark can influence splicing at this locus. In epithelial cells, FGFR2 expresses exon IIIb but excludes exon IIIc. Epithelial splicing regulatory protein (ESRP) is expressed and stimulates the inclusion of exon IIIb; reduced levels of H3K36me3 present at this exon, possibly as a result of lower SETD2 levels, allow its derepression. The role of dimethylases, such as the proteins of the nuclear receptor SET domain-containing (NSD) family, in this process has yet to be determined but these enzymes could also influence H3K36 methylation here.

Figure 4. Model for H3K36 methylation at sites of DNA damage

Upon the generation of DNA damage, SET domain and mariner transposase fusion gene- containing (SETMAR) dimethylates Lys36 on histone H3 (H3K36) near sites of DNA double-strand breaks (DSBs), possibly by recruiting currently undefined reader proteins that facilitate the binding of KU70 and the MRE11 RAD50 NBS1 (MRN) complex to facilitate DNA repair. How methylation at H3K36 is coordinated with other chromatin modifications that are known to participate in DNA repair (such as, p53-binding protein 1 (53BP1) binding to dimethylated H4K20 (H4K20me2)) is unknown. NSD2, nuclear receptor SET domain-containing 2.

Figure 5. NSD proteins can act as oncoproteins

Through overexpression and/or translocation events that result in the fusion of nuclear receptor SET domain-containing (NSD) proteins with other proteins, such as the nucleoporin NUP98, NSD proteins can be aberrantly recruited to target loci in various tissues. As a consequence, global levels of dimethylated Lys36 on histone H3 (H3K36me2) increase and are sufficient to activate inappropriate transcription, which contributes to cancer development. In some cases, the increased levels of H3K36me2 are expected to inversely correlate with trimethylated H3K27 (H3K27me3; not shown), altering the balance between competitive activating and repressive ‘marks’. As a consequence, multiple gene sets that are sensitive to the levels of H3K36me2 are turned on, a causal event in oncogenesis. AML, acute myeloid leukaemia; AR, androgen receptor; RNAPII, RNA polymerase II.