Journal of Biological Chemistry
Volume 276, Issue 36, 7 September 2001, Pages 33788-33797
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GENES: STRUCTURE AND REGULATION
Ssn6-Tup1 Regulates RNR3 by Positioning Nucleosomes and Affecting the Chromatin Structure at the Upstream Repression Sequence*

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The DNA damage inducible gene ribonucleotide reductase (RNR3) is regulated by a transcriptional repression mechanism by the recruitment of the Ssn6-Tup1 corepressor complex to its promoter by the sequence-specific DNA-binding protein Crt1. Ssn6-Tup1 is reported to represses transcription by interfering with transcription factors, recruiting histone deacetylases, and positioning nucleosomes at the promoter of its target genes. Two of the three mechanisms involve effects on chromatin structure, and therefore, we have delineated the nucleosomal structure of RNR3 in the repressed and derepressed state using multiple nuclease mapping strategies. A regular array of positioned nucleosomes is detected over the repressed RNR3 promoter that extends into the coding sequence. Treating cells with DNA damaging agents or deletingCRT1, SSN6, or TUP1 derepressesRNR3 transcription, and causes a dramatic disruption of nucleosome positioning over its promoter. Furthermore, derepression ofRNR3 correlated with changes in nuclease sensitivity within the upstream repression sequence (URS) region. Specifically, the loss of a MNase-hypersensitive site, and the appearance of strong DNase I hypersensitivity, was observed over the URS. Interestingly, we find that the binding of Crt1 to the promoter in the absence of Ssn6 or Tup1 is insufficient for nucleosome positioning or regulating chromatin structure at the URS; thus, these two functions are strictly dependent upon Ssn6-Tup1. We propose that RNR3 is regulated by changes in nucleosome positioning and chromatin structure that are mediated by Ssn6, Tup1, and Crt1.

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Published, JBC Papers in Press, July 11, 2001, DOI 10.1074/jbc.M104220200

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This work was supported by National Institutes of Health Grant GM58672 (to J. C. R.).The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.