title: Analysis of novel Sir3 binding regions in Saccharomyces cerevisiae.
abstract: In Saccharomyces cerevisiae, the HMR, HML, telomere and rDNA regions are silenced. Silencing at the rDNA region requires Sir2, and silencing at the HMR, HML and telomere regions requires binding of a protein complex, consisting of Sir2, Sir3 and Sir4, that mediates repression of gene expression. Here, several novel Sir3 binding domains, termed CN domains (Chromosomal Novel Sir3 binding region), were identified using chromatin immunoprecipitation (ChIP) on chip analysis of S. cerevisiae chromosomes. Furthermore, analysis of G1-arrested cells demonstrated that Sir3 binding was elevated in G1-arrested cells compared with logarithmically growing asynchronous cells, and that Sir3 binding varied with the cell cycle. In addition to 14 CN regions identified from analysis of logarithmically growing asynchronous cells (CN1-14), 11 CN regions were identified from G1-arrested cells (CN15-25). Gene expression at some CN regions did not differ between WT and sir3Δ strains. Sir3 at conventional heterochromatic regions is thought to be recruited to chromosomes by Sir2 and Sir4; however, in this study, Sir3 binding occurred at some CN regions even in sir2Δ and sir4Δ backgrounds. Taken together, our results suggest that Sir3 exhibits novel binding parameters and gene regulatory functions at the CN binding domains.
authors.affiliation: Department of Applied Chemistry & Biotechnology, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan;
authors.forename: Risa
authors.initials: R
authors.lastname: Mitsumori
authors.affiliation: Department of Applied Chemistry & Biotechnology, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan;
authors.forename: Tomoe
authors.initials: T
authors.lastname: Ohashi
authors.affiliation: Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan; Department of Frontier Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan;
authors.forename: Kazuto
authors.initials: K
authors.lastname: Kugou
authors.affiliation: Department of Applied Chemistry & Biotechnology, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan;
authors.forename: Ayako
authors.initials: A
authors.lastname: Ichino
authors.affiliation: Department of Applied Chemistry & Biotechnology, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan;
authors.forename: Kei
authors.initials: K
authors.lastname: Taniguchi
authors.affiliation: Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan;
authors.forename: Kunihiro
authors.initials: K
authors.lastname: Ohta
authors.affiliation: Department of Applied Chemistry & Biotechnology, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan;
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Uchida
authors.affiliation: Department of Applied Chemistry & Biotechnology, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan; Research and Education Program for Life Science, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan and PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan ma4sa6ya@u-fukui.ac.jp.
authors.forename: Masaya
authors.initials: M
authors.lastname: Oki
mesh_terms: D001665:Binding Sites; D002843:Chromatin / Q000235:genetics / Q000378:metabolism*; D015825:Chromosomes, Fungal / Q000235:genetics / Q000378:metabolism*; D059585:G1 Phase Cell Cycle Checkpoints / Q000502:physiology*; D015966:Gene Expression Regulation, Fungal / Q000502:physiology*; D011485:Protein Binding; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism*; D038281:Silent Information Regulator Proteins, Saccharomyces cerevisiae / Q000378:metabolism*
chemical_list: D002843:Chromatin; C084122:SIR3 protein, S cerevisiae; D038281:Silent Information Regulator Proteins, Saccharomyces cerevisiae
keywords: chromatin; gene expression; genome structure; histones; yeast