Molecular basis for oncohistone H3 recognition by SETD2 methyltransferase

Abstract

High-frequency point mutations of genes encoding histones have been identified recently as novel drivers in a number of tumors. Specifically, the H3K36M/I mutations were shown to be oncogenic in chondroblastomas and undifferentiated sarcomas by inhibiting H3K36 methyltransferases, including SETD2. Here we report the crystal structures of the SETD2 catalytic domain bound to H3K36M or H3K36I peptides with SAH (S-adenosylhomocysteine). In the complex structure, the catalytic domain adopts an open conformation, with the K36M/I peptide snuggly positioned in a newly formed substrate channel. Our structural and biochemical data reveal the molecular basis underying oncohistone recognition by and inhibition of SETD2.Supplemental material is available for this article.Received May 16, 2016; revised version accepted June 20, 2016. Histone post-translational modifications (PTMs) are linked to tumorigenesis, mostly via dysfunction of their regulators (e.g., readers, writers, and erasers) that are frequently mutated in tumors (Dawson and Kouzarides 2012). Recently, high-frequency mutations in genes encoding histones themselves, rather than the histone regulators, were identified in a number of cancer types. Exome sequencing studies have identified recurrent hot spot missense mutations in histone H3. Notably, these mutations are located at or adjacent to H3 lysine residues that undergo acetylation and/or methylation. For example, the H3K27M mutation was identified in the majority of pediatric diffuse intrinsic pontine gliomas (Schwartzentruber et al. 2012;Wu et al. 2012), and the H3K36M mutation was found to occur predominantly in chondroblastomas (Behjati et al. 2013) and rarely in other cancer types such as head and neck squamous cell carcinoma and colorectal cancer (Shah et al. 2014). In addition, the H3K36-neighboring G34 mutations, such as G34R/V and G34W/L, have been detected in pediatric non-brain stem gliomas (Schwartzentruber et al. 2012;Wu et al. 2012) and giant cell tumors of the bone (Behjati et al. 2013), respectively.Biochemical and cellular studies showed that H3K27M reduced global H3K27 methylation in vitro and in vivo by inhibiting the methyltransferase activity of polycombrepressive complex 2 (PRC2) (Chan et al. 2013;Lewis et al. 2013;Justin et al. 2016). Recently, we and others identified a similar "poisoning" mechanism underlying H3K36M-driven tumorigenesis involving the inactivation of H3K36 methyltransferases (Fang et al. 2016;Lu et al. 2016). H3K36 can be methylated by enzymes such as NSD1/2/3, ASH1L, and SETD2 (Wagner and Carpenter 2012). Among them, SETD2 serves as the major H3K36 methyltransferase that is able to generate the trimethylated H3K36 from the unmethylated, monomethylated, or dimethylated states in vitro and in cells (Edmunds et al. 2008;Hu et al. 2010). SETD2 plays important roles in cellular processes such as transcription elongation (Yoh et al. 2008), RNA splicing (de Almeida et al. 2011;Kim et al. 2011), and DNA damage repair (Li et al. 2013;Pai et al. 2014). However, due to the lack...

Shaping the cellular landscape with Set2/SETD2 methylation

“…Mutations at H3.3K36 result in genome-wide loss of H3K36 tri-methylation and can directly stimulate tumor formation [167, 168]. Similar to the mechanism by which K→M mutations at H3K9 and H3K27 “trap” or “poison” their respective methyltransferase enzymes [169–172], the H3.3K36M mutation rearranges the active center of SETD2 to provide a high affinity binding site for the H3.3K36M histone tail, thus explaining how a single histone mutation can impart a tumor phenotype [173]. As H3K36me is lost from the genome, a redistribution of H3K27me3 by PRC2 occurs across the genome [168].…”

The Histone Variant H3.3 in Transcriptional Regulation and Human Disease

“…Similar phenotypes were also observed in chondroblastoma cells that contain K36M mutations. Similar to K27M that sequesters EZH2, the K36M mutant inhibits H3K36 methyltransferases, including NSD1, NSD2 and SETD2 in vitro [118], and reduces global H3K36 methylation in vivo [119, 120]. Loss of H3K36 methylation leads to increased H3K27me3 in the intergenic regions, redistribution of the PRC1 complex from its target genes, and consequently, upregulation of PRC1-repressed target genes known to block mesenchymal differentiation [119].…”

Phosphorylation of the ancestral histone variant H3.3 amplifies stimulation-induced transcription

“…Structural studies of the SETD2 SET domain have revealed a basic patch along the path of the H3 amino-terminal tail as it extends from the catalytic site 23,24 . We speculated that such a feature could provide the basis of a specific enhanced interaction between SETD2 and H3.3S31ph nucleosome substrates and that these interactions might link the augmented enzymatic activity we observed to structural properties.…”