title: Global reorganization of budding yeast chromosome conformation in different physiological conditions.
abstract: The organization of the genome is nonrandom and important for correct function. Specifically, the nuclear envelope plays a critical role in gene regulation. It generally constitutes a repressive environment, but several genes, including the GAL locus in budding yeast, are recruited to the nuclear periphery on activation. Here, we combine imaging and computational modeling to ask how the association of a single gene locus with the nuclear envelope influences the surrounding chromosome architecture. Systematic analysis of an entire yeast chromosome establishes that peripheral recruitment of the GAL locus is part of a large-scale rearrangement that shifts many chromosomal regions closer to the nuclear envelope. This process is likely caused by the presence of several independent anchoring points. To identify novel factors required for peripheral anchoring, we performed a genome-wide screen and demonstrated that the histone acetyltransferase SAGA and the activity of histone deacetylases are needed for this extensive gene recruitment to the nuclear periphery.
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule Zurich, 8093 Zurich, Switzerland elisa.dultz@bc.biol.ethz.ch.
authors.forename: Elisa
authors.initials: E
authors.lastname: Dultz
authors.affiliation: Department of Biological Sciences, Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089.
authors.forename: Harianto
authors.initials: H
authors.lastname: Tjong
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720.
authors.forename: Elodie
authors.initials: E
authors.lastname: Weider
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720.
authors.forename: Mareike
authors.initials: M
authors.lastname: Herzog
authors.affiliation: Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T1Z3, Canada.
authors.forename: Barry
authors.initials: B
authors.lastname: Young
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720.
authors.forename: Christiane
authors.initials: C
authors.lastname: Brune
authors.affiliation: Department of Mathematics, Stanford University, Stanford, CA 94305.
authors.forename: Daniel
authors.initials: D
authors.lastname: Müllner
authors.affiliation: Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T1Z3, Canada.
authors.forename: Christopher
authors.initials: C
authors.lastname: Loewen
authors.affiliation: Department of Biological Sciences, Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089.
authors.forename: Frank
authors.initials: F
authors.lastname: Alber
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule Zurich, 8093 Zurich, Switzerland.
authors.forename: Karsten
authors.initials: K
authors.lastname: Weis
mesh_terms: D002843:Chromatin / Q000235:genetics* / Q000378:metabolism; D042002:Chromatin Assembly and Disassembly; D015825:Chromosomes, Fungal / Q000648:ultrastructure*; D003198:Computer Simulation; D005686:Galactokinase / Q000235:genetics / Q000378:metabolism; D005690:Galactose / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D015723:Gene Library; D005800:Genes, Fungal; D056426:Genetic Loci; D005947:Glucose / Q000378:metabolism; D006655:Histone Deacetylases / Q000378:metabolism; D008957:Models, Genetic; D009685:Nuclear Envelope / Q000378:metabolism / Q000648:ultrastructure*; D009690:Nucleic Acid Conformation; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism; D015534:Trans-Activators / Q000235:genetics / Q000378:metabolism
chemical_list: D002843:Chromatin; C518355:GAL10 protein, S cerevisiae; C507785:SAGA complex, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D015534:Trans-Activators; C524219:GAL1 protein, S cerevisiae; D005686:Galactokinase; D006655:Histone Deacetylases; D005947:Glucose; D005690:Galactose
references.citation: Nat Cell Biol. 2001 Feb;3(2):114-20
references.pmid: 11175742
references.citation: Prog Nucleic Acid Res Mol Biol. 2001;65:197-259
references.pmid: 11008489
references.citation: Science. 2001 Dec 14;294(5550):2364-8
references.pmid: 11743205
references.citation: J Biol Chem. 2002 Mar 8;277(10):7989-95
references.pmid: 11773077
references.citation: Nat Cell Biol. 2002 Mar;4(3):214-21
references.pmid: 11862215
references.citation: Cell. 2002 May 31;109(5):551-62
references.pmid: 12062099
references.citation: Funct Integr Genomics. 2002 Sep;2(4-5):181-92
references.pmid: 12192591
references.citation: Mol Cell Biol. 2002 Dec;22(23):8292-301
references.pmid: 12417731
references.citation: Nat Methods. 2008 Dec;5(12):1031-7
references.pmid: 18978785
references.citation: Curr Biol. 2002 Dec 23;12(24):2076-89
references.pmid: 12498682
references.citation: J Struct Biol. 2002 Oct-Dec;140(1-3):79-91
references.pmid: 12490156
references.citation: Nat Cell Biol. 2009 Sep;11(9):1109-15
references.pmid: 19684577
references.citation: Cell. 2004 Jan 9;116(1):75-86
references.pmid: 14718168
references.citation: EMBO J. 2004 Mar 24;23(6):1301-12
references.pmid: 15014445
references.citation: Cell. 2004 May 14;117(4):427-39
references.pmid: 15137937
references.citation: Nucleic Acids Res. 1993 Jul 11;21(14):3329-30
references.pmid: 8341614
references.citation: Cell. 1997 Oct 3;91(1):35-45
references.pmid: 9335333
references.citation: Yeast. 1998 Jul;14(10):943-51
references.pmid: 9717240
references.citation: Trends Genet. 1999 Jan;15(1):29-33
references.pmid: 10087931
references.citation: Science. 1999 Aug 6;285(5429):901-6
references.pmid: 10436161
references.citation: PLoS Biol. 2004 Nov;2(11):e342
references.pmid: 15455074
references.citation: J Cell Sci. 2005 Sep 1;118(Pt 17):4017-25
references.pmid: 16129885
references.citation: Nature. 2006 Jun 8;441(7094):770-3
references.pmid: 16760982
references.citation: Nature. 2006 Jun 8;441(7094):774-8
references.pmid: 16760983
references.citation: EMBO J. 2006 Sep 20;25(18):4253-62
references.pmid: 16946703
references.citation: Mol Cell Biol. 2006 Nov;26(21):7858-70
references.pmid: 16954382
references.citation: J Cell Biol. 2006 Nov 20;175(4):579-93
references.pmid: 17116750
references.citation: Mol Cell. 2007 Jan 12;25(1):31-42
references.pmid: 17218269
references.citation: J Biol Chem. 2007 Feb 2;282(5):3042-9
references.pmid: 17158105
references.citation: Nat Rev Mol Cell Biol. 2008 Mar;9(3):206-18
references.pmid: 18292778
references.citation: Genes Dev. 2008 Mar 1;22(5):627-39
references.pmid: 18316479
references.citation: Yeast. 2008 Mar;25(3):235-9
references.pmid: 18302313
references.citation: Nat Cell Biol. 2008 Jun;10(6):707-15
references.pmid: 18488019
references.citation: Mol Cell. 2008 Jul 11;31(1):104-13
references.pmid: 18614049
references.citation: Curr Protoc Cytom. 2004 Nov;Chapter 7:Unit 7.23
references.pmid: 18770800
references.citation: Mol Cell Biol. 2009 Nov;29(22):6033-45
references.pmid: 19737915
references.citation: Nat Cell Biol. 2010 Feb;12(2):111-8
references.pmid: 20098417
references.citation: Proc Natl Acad Sci U S A. 2010 Feb 2;107(5):2025-30
references.pmid: 20080699
references.citation: BMC Syst Biol. 2010;4:12
references.pmid: 20167065
references.citation: Curr Opin Cell Biol. 2010 Jun;22(3):374-82
references.pmid: 20363118
references.citation: Mol Biol Cell. 2010 Oct 1;21(19):3421-32
references.pmid: 20702586
references.citation: J Cell Biol. 2011 Apr 4;193(1):21-9
references.pmid: 21464227
references.citation: Mol Cell. 2011 May 20;42(4):426-37
references.pmid: 21596309
references.citation: PLoS Biol. 2012 Jan;10(1):e1001244
references.pmid: 22272186
references.citation: Mol Biol Cell. 2012 Apr;23(7):1367-75
references.pmid: 22323286
references.citation: J Biol Chem. 2012 Jun 22;287(26):22080-8
references.pmid: 22570481
references.citation: Genome Res. 2012 Jul;22(7):1295-305
references.pmid: 22619363
references.citation: Curr Biol. 2012 Oct 23;22(20):1881-90
references.pmid: 22940469
references.citation: Cell. 2013 Mar 14;152(6):1270-84
references.pmid: 23498936
references.citation: J Cell Biol. 2013 Jul 22;202(2):201-10
references.pmid: 23878273
references.citation: BMC Bioinformatics. 2013;14:354
references.pmid: 24305553
references.citation: Nucleic Acids Res. 2014 Jun;42(10):6686-97
references.pmid: 24705649
references.citation: Elife. 2014;3. doi: 10.7554/eLife.03790
references.pmid: 25402830
references.citation: Nat Rev Mol Cell Biol. 2015 Apr;16(4):245-57
references.pmid: 25757416
references.citation: Nature. 2000 Jan 6;403(6765):108-12
references.pmid: 10638763
references.citation: J Cell Sci. 2000 Jun;113 ( Pt 11):1903-12
references.pmid: 10806101
references.citation: Nature. 2000 Jun 8;405(6787):701-4
references.pmid: 10864329
references.citation: Genes Dev. 2001 Nov 15;15(22):2991-3004
references.pmid: 11711434