Histone H3 Lysine 36 Methylation Antagonizes Silencing in Saccharomyces cerevisiae Independently of the Rpd3S Histone Deacetylase Complex

Abstract

In yeast, methylation of histone H3 on lysine 36 (H3-K36) is catalyzed by the NSD1 leukemia oncoprotein homolog Set2. The histone deacetylase complex Rpd3S is recruited to chromatin via binding of the chromodomain protein Eaf3 to methylated H3-K36 to prevent erroneous transcription initiation. Here we identify a distinct function for H3-K36 methylation. We used random mutagenesis of histones H3 and H4 followed by a reporter-based screen to identify residues necessary to prevent the ectopic spread of silencing from the silent mating-type locus HMRa into flanking euchromatin. Mutations in H3-K36 or deletion of SET2 caused ectopic silencing of a heterochromatin-adjacent reporter. Transcriptional profiling revealed that telomere-proximal genes are enriched for those that display decreased expression in a set2D strain. Deletion of SIR4 rescued the expression defect of 26 of 37 telomere-proximal genes with reduced expression in set2D cells, implying that H3-K36 methylation prevents the spread of telomeric silencing. Indeed, Sir3 spreads from heterochromatin into neighboring euchromatin in set2D cells. Furthermore, genetic experiments demonstrated that cells lacking the Rpd3S-specific subunits Eaf3 or Rco1 did not display the anti-silencing phenotype of mutations in SET2 or H3-K36. Thus, antagonism of silencing is independent of the only known effector of this conserved histone modification.

Rpd3-dependent boundary formation at telomeres by removal of Sir2 substrate

“…However, set2Δ does not cause a growth defect in sas2Δ cells (Fig. 1C), indicating that neither Set2-dependent recruitment of Rpd3 (S) (20) nor an Rpd3(S)-independent function of Set2 at telomere boundaries (29) is involved in the synthetic lethality between sas2Δ and rpd3Δ. The lethality is reflected further in an increased sensitivity of sas2Δ cells to treatment with the HDAC inhibitor trichostatin A (Fig.…”

The Brd4 Extraterminal Domain Confers Transcription Activation Independent of pTEFb by Recruiting Multiple Proteins, Including NSD3

“…NSD3, also known as WHSC1L1, is a histone methyltransferase that belongs to the mammalian NSD family of SET domain-containing methyltransferases, which have been shown to catalyze H3K36 methylation (30,36). Studies ranging from yeast to humans suggest that methylated H3K36 is enriched in regions of active transcription and is linked to transcriptional elongation and productive transcription within coding regions (5,48,49,53). To explore the mechanism by which NSD3 contributes to the transcription activation of Brd4 target genes, we next asked whether the Brd4/ NSD3 complex regulates H3K36 methylation levels at Brd4 target genes.…”

“…The SET domain of NSD proteins is homologous to the Saccharomyces cerevisiae histone-3 lysine-36 (H3K36)-specific methyltransferase SET2 and is specific for H3K36 dimethylation (H3K36me2) (30). Studies ranging from yeast to humans suggest that methylated H3K36 is enriched in regions of active transcription and is linked to transcriptional elongation and productive transcription within coding regions (5,48,49,53).…”

Telomere as an Important Player in Regulation of Microbial Pathogen Virulence

“…As an antagonizing effect, methylation of H3K79 by Dot1 will prevent Sir3 from binding the nucleosome . Similarly, Set1 and Set2 methylates H3 on K4 and K36 residues, respectively (Krogan et al 2002;Nagy et al 2002;Roguev et al 2001;Strahl et al 2002), and methylated histone H3 prevents Sir4 from binding the nucleosome (Tompa & Madhani 2007;Venkatasubrahmanyam et al 2007). Therefore, binding of Sir3 and Sir4 recruits Sir2, which deacetylates neighboring histone tails and allows subsequent binding of Sir3 and Sir4 to neighboring nucleosome.…”