A conserved genetic interaction between Spt6 and Set2 regulates H3K36 methylation.

Rajaraman Gopalakrishnan,Robert E Kingston,Sharon K Marr,Fred Winston

doi:10.1093/nar/gkz119

Rajaraman Gopalakrishnan, Robert E Kingston + Show 2 more

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https://doi.org/10.1093/nar/gkz119

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Abstract

The transcription elongation factor Spt6 and the H3K36 methyltransferase Set2 are both required for H3K36 methylation and transcriptional fidelity in Saccharomyces cerevisiae. However, the nature of the requirement for Spt6 has remained elusive. By selecting for suppressors of a transcriptional defect in an spt6 mutant, we have isolated several highly clustered, dominant SET2 mutations (SET2sup mutations) in a region encoding a proposed autoinhibitory domain. SET2sup mutations suppress the H3K36 methylation defect in the spt6 mutant, as well as in other mutants that impair H3K36 methylation. We also show that SET2sup mutations overcome the requirement for certain Set2 domains for H3K36 methylation. In vivo, SET2sup mutants have elevated levels of H3K36 methylation and the purified Set2sup mutant protein has greater enzymatic activityin vitro. ChIP-seq studies demonstrate that the H3K36 methylation defect in the spt6 mutant, as well as its suppression by a SET2sup mutation, occurs at a step following the recruitment of Set2 to chromatin. Other experiments show that a similar genetic relationship between Spt6 and Set2 exists in Schizosaccharomyces pombe. Taken together, our results suggest a conserved mechanism by which the Set2 autoinhibitory domain requires multiple Set2 interactions to ensure that H3K36 methylation occurs specifically on actively transcribed chromatin.

Highlights

The histone chaperone Spt[6] is a highly conserved transcription elongation factor required for many aspects of transcription and chromatin structure
Isolation and analysis of dominant SET2 mutations that suppress intragenic transcription in an spt6-1004 mutant To identify factors that regulate intragenic transcription, we selected for mutations that suppress this class of transcription in an spt6-1004 mutant[21], which allows extensive intragenic transcription[22,23]
SET2sup mutations suppress the loss of Set[2] domains normally required for its catalytic activity We investigated whether SET2sup mutations suppress the loss of two Set[2] regulatory domains required for Set[2] activity: the SRI domain, which binds to the RNA polymerase II (RNAPII) CTD19,46, and the HB domain, required for interaction with histones H2A and H443

Summary

Introduction

The histone chaperone Spt[6] is a highly conserved transcription elongation factor required for many aspects of transcription and chromatin structure. Set[2] normally represses intragenic transcription via its association with RNAPII during transcription elongation, resulting in H3K36me2/me[3] over gene bodies[32,33,34]. This histone modification is required for the co-transcriptional function of the Rpd3S histone deacetylase complex[17,35,36,37,38]. Regulation of intragenic transcription by H3K36 methylation is conserved as depletion of SETD2 (a human orthologue of yeast SET2) results in the genome-wide expression of intragenic transcripts[39]

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