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 ( SET2 sup mutations) in a region encoding a proposed autoinhibitory domain. SET2 sup mutations suppress the H3K36 methylation defect in the spt6 mutant, as well as in other mutants that impair H3K36 methylation. We also show that SET2 sup mutations overcome the requirement for certain Set2 domains for H3K36 methylation. In vivo, SET2 sup mutants have elevated levels of H3K36 methylation and the purified Set2 sup mutant protein has greater enzymatic activity in vitro . ChIP-seq studies demonstrate that the H3K36 methylation defect in the spt6 mutant, as well as its suppression by a SET2 sup 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.

2The transcription elongation factor Spt6 and the H3K36 methyltransferase Set2 are both required for H3K36 methylation and transcriptional fidelity in Saccharomyces cerevisiae. By selecting for suppressors of a transcriptional defect in an spt6 mutant, we have isolated dominant SET2 mutations (SET2 sup mutations) in a region encoding a proposed autoinhibitory domain. The SET2 sup mutations suppress the H3K36 methylation defect in the spt6 mutant, as well as in other mutants that impair H3K36 methylation. ChIP-seq studies demonstrate that the H3K36 methylation defect in the spt6 mutant, as well as its suppression by a SET2 sup mutation, occur 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 interactions to ensure that H3K36 methylation occurs specifically on actively transcribed chromatin.. CC-BY-NC-ND 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/364521 doi: bioRxiv preprint first posted online Jul. 8, 2018; 3 IntroductionThe histone chaperone Spt6 is a highly conserved transcription elongation factor required for many aspects of transcription and chromatin structure. Spt6 binds directly to Rpb1, the largest subunit of RNA polymerase II (RNAPII) [1][2][3][4][5][6] , to histones and nucleosomes [7][8][9] , and to the essential transcription factor Spn1/Iws1 9-12 . Mutations in S. cerevisiae SPT6 cause genome-wide changes in histone occupancy [13][14][15][16] and impair several histone modifications, including H3K36 di-and trimethylation (H3K36me2/me3) catalyzed by the H3K36 methyltransferase Set2 [17][18][19][20] . Mutations in SPT6 also cause greatly elevated levels of transcripts that arise from within coding regions on both sense and antisense strands, known as intragenic transcription 15,[21][22][23][24] . Intragenic transcription has recently emerged as a mechanism to express alternative genetic information within a coding region (for example, [25][26][27][28][29] ).Regulation of intragenic transcription by Spt6 occurs, at least in part, by its regulation of H3K36 methylation, as a deletion of SET2 also causes genome-wide expression of intragenic transcripts 17,30,31 . Set2 normally represses intragenic transcription via its association with RNAPII during transcription elongation, resulting in H3K36me2/me3 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] . Deacetylation by Rpd3S over transcribed regions is believed to maintain a repressive environment that prevents intragenic transcription. Regulation of intragenic transcription by H3K36 methylation is co...

The budding yeast, Saccharomyces cerevisiae, has been widely used for genetic studies of fundamental cellular functions. The isolation and analysis of yeast mutants is a commonly used and powerful technique to identify the genes that are involved in a process of interest. Furthermore, natural genetic variation among wild yeast strains has been studied for analysis of polygenic traits by quantitative trait loci mapping. Whole‐genome sequencing, often combined with bulk segregant analysis, is a powerful technique that helps determine the identity of mutations causing a phenotype. Here, we describe protocols for the construction of libraries for S. cerevisiae whole‐genome sequencing. We also present a bioinformatic pipeline to determine the genetic variants in a yeast strain using whole‐genome sequencing data. This pipeline can also be used for analyzing Schizosaccharomyces pombe mutants. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: Generation of haploid spores for bulk segregant analysis Basic Protocol 2: Extraction of genomic DNA from yeast cells Basic Protocol 3: Shearing of genomic DNA for library preparation Basic Protocol 4: Construction and amplification of DNA libraries Support Protocol 1: Annealing oligonucleotides for forming Y‐adapters Support Protocol 2: Size selection and cleanup using SPRI beads Basic Protocol 5: Identification of genomic variants from sequencing data

The histone chaperone Spt6 is involved in promoting elongation of RNA polymerase II (RNAPII), maintaining chromatin structure, regulating co-transcriptional histone modifications, and controlling mRNA processing. These diverse functions of Spt6 are partly mediated through its interactions with RNAPII and other factors in the transcription elongation complex. In this study, we used mass spectrometry to characterize the differences in RNAPII interacting factors between wild-type cells and those depleted for Spt6, leading to the identification of proteins that depend on Spt6 for their interaction with RNAPII. The altered association of some of these factors could be attributed to changes in steady-state protein levels. However, Abd1, the mRNA cap methyltransferase, had decreased association with RNAPII after Spt6 depletion despite unchanged Abd1 protein levels, showing a requirement for Spt6 in mediating the Abd1-RNAPII interaction. Genome-wide studies showed that Spt6 is required for maintaining the level of Abd1 over transcribed regions, as well as the level of Spt5, another protein known to recruit Abd1 to chromatin. Abd1 levels were particularly decreased at the 5 ends of genes after Spt6 depletion, suggesting a greater need for Spt6 in Abd1 recruitment over these regions. Together, our results show that Spt6 is important in regulating the composition of the transcription elongation complex and reveal a previously unknown function for Spt6 in the recruitment of Abd1.