S-phase-independent silencing establishment in Saccharomyces cerevisiae

  1. Davis Goodnight
  2. Jasper Rine  Is a corresponding author
  1. University of California, Berkeley, United States


The establishment of silent chromatin, a heterochromatin-like structure at HML and HMR in Saccharomyces cerevisiae, depends on progression through S phase of the cell cycle, but the molecular nature of this requirement has remained elusive despite intensive study. Using high-resolution chromatin immunoprecipitation and single-molecule RNA analysis, we found that silencing establishment proceeded via gradual repression of transcription in individual cells over several cell cycles, and that the cell-cycle-regulated step was downstream of Sir protein recruitment. In contrast to prior results, HML and HMR had identical cell-cycle requirements for silencing establishment, with no apparent contribution from a tRNA gene adjacent to HMR. We identified the cause of the S-phase requirement for silencing establishment: removal of transcription-favoring histone modifications deposited by Dot1, Sas2, and Rtt109. These results revealed that silencing establishment was absolutely dependent on the cell-cycle-regulated interplay between euchromatic and heterochromatic histone modifications.

Data availability

Sequencing data have been deposited in the GEO under the accession number GSE150737.

The following data sets were generated

Article and author information

Author details

  1. Davis Goodnight

    Molecular & Cell Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5423-1424
  2. Jasper Rine

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    For correspondence
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2297-9814


National Institutes of Health (R01 GM31105)

  • Jasper Rine

National Institutes of Health (R01 GM120374)

  • Jasper Rine

National Institutes of Health (T32 GM007127)

  • Davis Goodnight

National Institutes of Health (T32 HG000047)

  • Davis Goodnight

National Science Foundation (Graduate Research Fellowship,1752814)

  • Davis Goodnight

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Tim Formosa, University of Utah School of Medicine, United States

Version history

  1. Received: May 14, 2020
  2. Accepted: July 18, 2020
  3. Accepted Manuscript published: July 20, 2020 (version 1)
  4. Version of Record published: August 3, 2020 (version 2)


© 2020, Goodnight & Rine

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.


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  1. Davis Goodnight
  2. Jasper Rine
S-phase-independent silencing establishment in Saccharomyces cerevisiae
eLife 9:e58910.

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