Methylation of Histone H3 by Set2 in Saccharomyces cerevisiae Is Linked to Transcriptional Elongation by RNA Polymerase II

Banting and Best Department of Medical Research, Toronto Yeast Proteomics Organization, University of Toronto, Toronto, Ontario, Canada M5G 1L6.
Molecular and Cellular Biology (Impact Factor: 4.78). 07/2003; 23(12):4207-18. DOI: 10.1128/MCB.23.12.4207-4218.2003
Source: PubMed


Set2 methylates Lys36 of histone H3. We show here that yeast Set2 copurifies with RNA polymerase II (RNAPII). Chromatin immunoprecipitation
analyses demonstrated that Set2 and histone H3 Lys36 methylation are associated with the coding regions of several genes that
were tested and correlate with active transcription. Both depend, as well, on the Paf1 elongation factor complex. The C terminus
of Set2, which contains a WW domain, is also required for effective Lys36 methylation. Deletion of CTK1, encoding an RNAPII CTD kinase, prevents Lys36 methylation and Set2 recruitment, suggesting that methylation may be triggered
by contact of the WW domain or C terminus of Set2 with Ser2-phosphorylated CTD. A set2 deletion results in slight sensitivity to 6-azauracil and much less β-galactosidase produced by a reporter plasmid, resulting
from a defect in transcription. In synthetic genetic array (SGA) analysis, synthetic growth defects were obtained when a set2 deletion was combined with deletions of all five components of the Paf1 complex, the chromodomain elongation factor Chd1,
the putative elongation factor Soh1, the Bre1 or Lge1 components of the histone H2B ubiquitination complex, or the histone
H2A variant Htz1. SET2 also interacts genetically with components of the Set1 and Set3 complexes, suggesting that Set1, Set2, and Set3 similarly
affect transcription by RNAPII.

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Available from: Minkyu Kim, Aug 14, 2014
    • "RESULTS PAF1 Depletion Leads to a Redistribution of Pol II from Promoters to Gene Bodies PAF1 was identified as a factor co-purifying with RNA Pol II (Shi et al., 1996; Wade et al., 1996), and in vitro approaches have shown that PAF1 can facilitate transcription elongation cooperatively with TFIIS, DSIF, and Tat-SF1 (Chen et al., 2009; Kim et al., 2010). Furthermore, in yeast, we demonstrated that PAF1 functions by regulating histone modifications associated with elongating forms of Pol II (Krogan et al., 2003). To identify factors required for the regulation of release of promoter-proximal paused Pol II, we set up an RNAi screen of Pol II elongation factors followed by Pol II ChIP-seq. "
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    ABSTRACT: The control of promoter-proximal pausing and the release of RNA polymerase II (Pol II) is a widely used mechanism for regulating gene expression in metazoans, especially for genes that respond to environmental and developmental cues. Here, we identify that Pol-II-associated factor 1 (PAF1) possesses an evolutionarily conserved function in metazoans in the regulation of promoter-proximal pausing. Reduction in PAF1 levels leads to an increased release of paused Pol II into gene bodies at thousands of genes. PAF1 depletion results in increased nascent and mature transcripts and increased levels of phosphorylation of Pol II's C-terminal domain on serine 2 (Ser2P). These changes can be explained by the recruitment of the Ser2P kinase super elongation complex (SEC) effecting increased release of paused Pol II into productive elongation, thus establishing PAF1 as a regulator of promoter-proximal pausing by Pol II. Copyright © 2015 Elsevier Inc. All rights reserved.
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    • "Histone H2B ubiquitination ( H2Bub ) at lysine123 is an important modification which functions during transcription initiation ( Henry et al . , 2003 ; Kao et al . , 2004 ) , and is critical for methylation of H3K4 and H3K79 by Set1 and Dot1 respectively ( Briggs et al . , 2002 ; Dover et al . , 2002 ; Krogan et al . , 2003 ; Ng et al . , 2003 ; Sun and Allis , 2002 ) ."
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    ABSTRACT: Cmr1 (Changed mutation rate) is a histone interacting, WD40 domain containing protein, with a previously identified role in the DNA damage repair pathway. Recent interest in Cmr1 has suggested roles in additional cellular processes. The current study was carried out to determine whether Cmr1 is involved in Pol II mediated transcription. Results presented herein provide the first evidence that Cmr1 is recruited to the coding regions of Pol II transcribed genes. It is recruited to the 5’ open reading frame in a manner dependent on Ser5 phosphorylation of the Pol II carboxyl terminal domain by the kinase Kin28. Strong evidence is provided that a primary function of Cmr1 is to coordinate recruitment and retention of the multifunctional elongation factor Paf1. Cmr1 was observed to occupy the coding region of the inducible genes ARG1 and HIS4 at significant levels, but not that of the constitutively expressed genes ADH1 and PMA1, suggesting that it regulates a subset of the multiple functions identified for Paf1. Additionally, it is important for efficient recruitment of the histone chaperone complex FACT and of the mRNA processing factor Rna14, both of which are consistent with previously identified roles for Paf1.
    Full-text · Thesis · Jun 2014
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    • "Histone H3K36 methylation has been extensively studied in yeast [25] and Drosophila [38], [39], where it is associated with transcription elongation. In yeast, H3K36 methylation is mediated by Set2 (histone lysine methyltransferase), which has been found to be associated with the elongation-competent form of RNA polymerase II [40], [41]. Transcription is a three-stage process consisting of initiation, elongation and termination; each stage requires a specific set of regulatory factors [42], [43]. "
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    ABSTRACT: Histone H3 lysine 36 (H3K36) methylation is known to be associated with transcriptionally active genes, and is considered a genomic marker of active loci. To investigate the changes in H3K36 methylation in pig, we determined the mono-, di-, and tri-methylations of H3K36 (H3K36me1, H3K36me2 and H3K36me3, respectively) in porcine fetal fibroblasts, oocytes and preimplantation embryos by immunocytochemistry using specific antibodies and confocal microscopy. These analyses revealed that only H3K36me3 in porcine fetal fibroblasts consistently colocalized with transcription sites identified as actively synthesizing RNA based on fluorouridine (FU) incorporation. Treatment of cells with flavopiridol, which blocks transcription elongation, completely abrogated both H3K36me3 signals and RNA synthesis. All three types of H3K36 methylation were present and did not significantly differ during oocyte maturation. In parthenogenetic embryos, H3K36me1 and -me2 were detected in 1-cell through blastocyst-stage embryos. In contrast, H3K36me3 was not detected in most 1-cell stage embryos. H3K36me3 signals became detectable in 2-cell stage embryos, peaked at the 4-cell stage, decreased at the 8-cell stage, and then became undetectable at blastocyst stages in both parthenogenetic and in vitro-fertilized (IVF) embryos. Unlike the case in IVF embryos, H3K36me3 could not be demethylated completely during the 1-cell stage in somatic cell nuclear transfer (SCNT) embryos. These results collectively indicate that H3K36me3, but not H3K36me1 or -me2, is associated with transcription elongation in porcine fetal fibroblasts. H3K36me3 is developmentally regulated and may be a histone mark of embryonic gene activation in pig. Aberrant H3K36 tri-methylation occurred during the nuclear reprogramming of SCNT embryos.
    Full-text · Article · Jun 2014 · PLoS ONE
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