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Modulation of mRNA and lncRNA expression dynamics by the Set2–Rpd3S pathway

Author

Listed:
  • Ji Hyun Kim

    (Ewha Womans University
    The Research Center for Cellular Homeostasis, Ewha Womans University)

  • Bo Bae Lee

    (Ewha Womans University
    The Research Center for Cellular Homeostasis, Ewha Womans University)

  • Young Mi Oh

    (Ewha Womans University
    The Research Center for Cellular Homeostasis, Ewha Womans University)

  • Chenchen Zhu

    (Genome Biology Unit, European Molecular Biology Laboratory
    Stanford Genome Technology Center, Stanford University School of Medicine
    Stanford University School of Medicine)

  • Lars M. Steinmetz

    (Genome Biology Unit, European Molecular Biology Laboratory
    Stanford Genome Technology Center, Stanford University School of Medicine
    Stanford University School of Medicine)

  • Yookyeong Lee

    (Ewha Womans University)

  • Wan Kyu Kim

    (Ewha Womans University)

  • Sung Bae Lee

    (DGIST)

  • Stephen Buratowski

    (Harvard Medical School)

  • TaeSoo Kim

    (Ewha Womans University
    The Research Center for Cellular Homeostasis, Ewha Womans University)

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.

Suggested Citation

  • Ji Hyun Kim & Bo Bae Lee & Young Mi Oh & Chenchen Zhu & Lars M. Steinmetz & Yookyeong Lee & Wan Kyu Kim & Sung Bae Lee & Stephen Buratowski & TaeSoo Kim, 2016. "Modulation of mRNA and lncRNA expression dynamics by the Set2–Rpd3S pathway," Nature Communications, Nature, vol. 7(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms13534
    DOI: 10.1038/ncomms13534
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    Cited by:

    1. Jonathan W. Markert & Seychelle M. Vos & Lucas Farnung, 2023. "Structure of the complete Saccharomyces cerevisiae Rpd3S-nucleosome complex," Nature Communications, Nature, vol. 14(1), pages 1-11, December.

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