Advertisement
Research Article

Systematic Dissection of Roles for Chromatin Regulators in a Yeast Stress Response

  • Assaf Weiner equal contributor,

    equal contributor Contributed equally to this work with: Assaf Weiner, Hsiuyi V. Chen

    Affiliations: School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel

    X
  • Hsiuyi V. Chen equal contributor,

    equal contributor Contributed equally to this work with: Assaf Weiner, Hsiuyi V. Chen

    Affiliation: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America

    X
  • Chih Long Liu,

    Affiliation: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America

    X
  • Ayelet Rahat,

    Affiliations: School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel

    X
  • Avital Klien,

    Affiliations: School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel

    X
  • Luis Soares,

    Affiliation: Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America

    X
  • Mohanram Gudipati,

    Affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America

    X
  • Jenna Pfeffner,

    Affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

    X
  • Aviv Regev,

    Affiliations: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America

    X
  • Stephen Buratowski,

    Affiliation: Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America

    X
  • Jeffrey A. Pleiss,

    Affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America

    X
  • Nir Friedman mail,

    nir@cs.huji.ac.il (NF); Oliver.Rando@umassmed.edu (OJR)

    Affiliations: School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel

    X
  • Oliver J. Rando mail

    nir@cs.huji.ac.il (NF); Oliver.Rando@umassmed.edu (OJR)

    Affiliation: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America

    X
  • Published: July 31, 2012
  • DOI: 10.1371/journal.pbio.1001369

Reader Comments (1)

Post a new comment on this article

Set1 and rDNA silencing

Posted by pmilkereit on 03 Sep 2012 at 13:52 GMT

Together with prior observations demonstrating a role for Set1 in rDNA silencing [62],[63] during midlog growth in YPD, our results therefore identify Set1 as a general repressor of ribosomal biogenesis, with roles in repressing rRNA, ribosomal protein genes, and ribosomal biogenesis genes.
http://plosbiology.org/article/info:doi/10.1371/journal.pbio.1001369#article1.body1.sec3.sec3.p2

Already in the results part you refer to “prior observations that Set1 is required for full repression of the rRNA repeats [62],[63] during steady-state growth (when a subset of rDNA repeats are silenced)”. Could you help to clarify the point whether these statements are about silencing of RNA polymerase ii transcribed genes in the yeast rDNA locus or about repression of the RNA polymerase I and RNA polymerase III transcribed (5S + 35S) rRNA genes?

No competing interests declared.

RE: Set1 and rDNA silencing

orando replied to pmilkereit on 04 Sep 2012 at 18:33 GMT

Sorry for the sloppy language. The two citations listed specifically investigated Pol2-dependent phenomena in the rDNA repeats, based on reporter silencing and suppression of transposon mobilization. One of the citations has a supplemental figure arguing against a Set1 effect on rRNA.

Given the antagonism between Pol I and Pol II within the rDNA repeats, and given reports of PHF8 regulating rRNA expression in response to H3K4me3, I would not be surprised if detailed investigation showed a (likely positive) role for Set1 in PolI transcription at these repeats.

All of that said, your comment is right on the mark -- those papers focused on "rDNA silencing", which refers to silencing of PolII transcription within the rDNAs.

No competing interests declared.

RE: RE: Set1 and rDNA silencing

pmilkereit replied to orando on 10 Sep 2012 at 14:08 GMT

Thanks for the clarification ...

No competing interests declared.