Histone H3K36 trimethylation is essential for multiple silencing mechanisms in fission yeast

Abstract

In budding yeast, Set2 catalyzes di- and trimethylation of H3K36 (H3K36me2 and H3K36me3) via an interaction between its Set2–Rpb1 interaction (SRI) domain and C-terminal repeats of RNA polymerase II (Pol2) phosphorylated at Ser2 and Ser5 (CTD-S2,5-P). H3K36me2 is sufficient for recruitment of the Rpd3S histone deacetylase complex to repress cryptic transcription from transcribed regions. In fission yeast, Set2 is also responsible for H3K36 methylation, which represses a subset of RNAs including heterochromatic and subtelomeric RNAs, at least in part via recruitment of Clr6 complex II, a homolog of Rpd3S. Here, we show that CTD-S2P-dependent interaction of fission yeast Set2 with Pol2 via the SRI domain is required for formation of H3K36me3, but not H3K36me2. H3K36me3 silenced heterochromatic and subtelomeric transcripts mainly through post-transcriptional and transcriptional mechanisms, respectively, whereas H3K36me2 was not enough for silencing. Clr6 complex II appeared not to be responsible for heterochromatic silencing by H3K36me3. Our results demonstrate that H3K36 methylation has multiple outputs in fission yeast; these findings provide insights into the distinct roles of H3K36 methylation in metazoans, which have different enzymes for synthesis of H3K36me1/2 and H3K36me3.

The Histone Acetyltransferase Mst2 Protects Active Chromatin from Epigenetic Silencing by Acetylating the Ubiquitin Ligase Brl1

“…In further support of the latter, it was previously reported that deletion of set2 + or pdp3 + alleviated heterochromatin silencing (Braun et al., 2011, Chen et al., 2008, Creamer et al., 2014, Matsuda et al., 2015, Suzuki et al., 2016) (Figure S2C). To test this more directly, we inhibited Mst2 recruitment to active genes using pdp3 Δ cells, and we analyzed the effect on silencing of heterochromatic genes.…”

“…Importantly, it functions to sequester Mst2 on transcriptionally active genes, which serves a dual purpose: (1) it fuels the euchromatic positive feedback loop described above, and (2) it prevents Mst2 from acting promiscuously on constitutive heterochromatin. Thereby, H3K36me3 maintains euchromatic genes in an active state, and it concurrently safeguards constitutive heterochromatin from illegitimate activation by an invasion of Mst2, providing an explanation for the previously reported silencing defects in set2 + -deficient cells (Chen et al., 2008, Creamer et al., 2014, Matsuda et al., 2015, Suzuki et al., 2016). …”

A demethylation deficient isoform of the lysine demethylase KDM2A interacts with pericentromeric heterochromatin in an HP1a-dependent manner

“…2,[6][7][8] Although H3K36me3 and H3K36me2 are associated mainly with active gene bodies, where they prevent spurious transcription initiations, H3K36me2 has been also found to be associated with transcriptionally active gene promoters and its removal by KDM2A leads to transcriptional repression of such promoters. 1,[9][10][11][12][13][14][15][16][17][18][19] The short demethylation-defiecient KDM2A isoform KDM2A-SF lacks the N-terminal demethylation domain, but it retains the ability to bind to CpG islands. 15,23,24 KDM2A-SF is therefore likely to compete with KDM2A-LF for the same CpG islands.…”

“…2,[6][7][8] Although methylation of H3K36 is known to repress spurious transcription initiation in bodies of transcriptionally active genes and it has been detected on promoters of transcriptionally repressed genes, H3K36me2 has been also shown to be associated with transcriptionally active promoters. 2,[9][10][11][12][13][14][15] Demethylation of promoter-associated H3K36me2 by KDM2A has been shown to result in transcriptional repression of these promoters, whereas a loss of KDM2A leads to increased levels of promoter-associated H3K36me2 and transcriptional de-repression of these promoters. 10,14,[16][17][18][19] KDM2A also demethylates lysine residues of non-histone proteins such as the NF-kB p65 subunit or b-catenin.…”

Epigenetic gene regulation by histone demethylases: emerging role in oncogenesis and inflammation

“… a Wang et al (2014); b Lloret-Llinares et al (2012); c Lauberth et al (2013); d Chen et al (2015); e Audergon et al (2015); f Zhu et al (2010); g El Gazzar et al (2008); h Arnoult et al (2012); i Deng et al (2015); j De Santa et al (2009); k Agger et al (2009); l Tanaka et al (2015); m Suzuki et al (2016); n Sen et al (2015); o Jack et al (2013); p Jørgensen et al (2013); q Shinchi et al (2015); r Stender et al , 2012. …”