title: Modulation of mRNA and lncRNA expression dynamics by the Set2-Rpd3S pathway.
abstract: H3K36 methylation by Set2 targets Rpd3S histone deacetylase to transcribed regions of mRNA genes, repressing internal cryptic promoters and slowing elongation. Here we explore the function of this pathway by analysing transcription in yeast undergoing a series of carbon source shifts. Approximately 80 mRNA genes show increased induction upon SET2 deletion. A majority of these promoters have overlapping lncRNA transcription that targets H3K36me3 and deacetylation by Rpd3S to the mRNA promoter. We previously reported a similar mechanism for H3K4me2-mediated repression via recruitment of the Set3C histone deacetylase. Here we show that the distance between an mRNA and overlapping lncRNA promoter determines whether Set2-Rpd3S or Set3C represses. This analysis also reveals many previously unreported cryptic ncRNAs induced by specific carbon sources, showing that cryptic promoters can be environmentally regulated. Therefore, in addition to repression of cryptic transcription and modulation of elongation, H3K36 methylation maintains optimal expression dynamics of many mRNAs and ncRNAs.
authors.affiliation: Department of Life Science, Ewha Womans University, Seoul 03760, Korea.|The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea.
authors.forename: Ji Hyun
authors.initials: JH
authors.lastname: Kim
authors.affiliation: Department of Life Science, Ewha Womans University, Seoul 03760, Korea.|The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea.
authors.forename: Bo Bae
authors.initials: BB
authors.lastname: Lee
authors.affiliation: Department of Life Science, Ewha Womans University, Seoul 03760, Korea.|The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea.
authors.forename: Young Mi
authors.initials: YM
authors.lastname: Oh
authors.affiliation: Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.|Stanford Genome Technology Center, Stanford University School of Medicine, Stanford, California 94305, USA.|Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.
authors.forename: Chenchen
authors.initials: C
authors.lastname: Zhu
authors.affiliation: Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.|Stanford Genome Technology Center, Stanford University School of Medicine, Stanford, California 94305, USA.|Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.
authors.forename: Lars M
authors.initials: LM
authors.lastname: Steinmetz
authors.affiliation: Department of Life Science, Ewha Womans University, Seoul 03760, Korea.
authors.forename: Yookyeong
authors.identifier: 0000-0003-0367-4652
authors.initials: Y
authors.lastname: Lee
authors.affiliation: Department of Life Science, Ewha Womans University, Seoul 03760, Korea.
authors.forename: Wan Kyu
authors.initials: WK
authors.lastname: Kim
authors.affiliation: Department of Brain and Cognitive Sciences, DGIST, Daegu 42988, Korea.
authors.forename: Sung Bae
authors.initials: SB
authors.lastname: Lee
authors.affiliation: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Stephen
authors.identifier: 0000-0003-0440-3926
authors.initials: S
authors.lastname: Buratowski
authors.affiliation: Department of Life Science, Ewha Womans University, Seoul 03760, Korea.|The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea.
authors.forename: TaeSoo
authors.initials: T
authors.lastname: Kim
mesh_terms: D015966:Gene Expression Regulation, Fungal; D006657:Histones / Q000378:metabolism; D007700:Kinetics; D008239:Lysine / Q000378:metabolism; D008745:Methylation; D008780:Methyltransferases / Q000378:metabolism*; D008954:Models, Biological; D011401:Promoter Regions, Genetic / Q000235:genetics; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D006657:Histones; D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D029701:Saccharomyces cerevisiae Proteins; D008780:Methyltransferases; C448996:Set2 protein, S cerevisiae; D008239:Lysine