title: Direct regulation of nucleosome density by the conserved AAA-ATPase Yta7.
abstract: Yta7 is a highly conserved bromodomain-containing protein with AAA-ATPase homology originally implicated in heterochromatin boundary function in Saccharomyces cerevisiae. Although increased activity of the human ortholog has been implicated in malignant breast tumors, Yta7's precise mode of action is unknown. Transcriptional analysis in yeast cells revealed a role for Yta7 and its ATPase function in gene induction, including galactose- and sporulation-induced transcription. This requirement was direct and activating, because Yta7 associated with the GAL gene cluster only upon transcriptional induction. Suggestive of a role in transcriptional elongation, Yta7 localized to the ORFs of highly transcribed genes. Intriguingly, the yta7Δ mutant's transcriptional defects were partially suppressed by decreased dosage of histones H3 and H4. Consistent with this suppression, cells lacking Yta7 exhibited both increased levels of chromatin-incorporated histone H3 and decreased nucleosome spacing. Importantly, this modulation of H3 levels occurred independently of changes in H3 transcript level. Because Yta7 binds histone H3 in vitro, these results suggested a direct role for Yta7 in H3 eviction or degradation. Further, local loss of Yta7 activity at a long inducible gene resulted in accumulation of H3 at the 3' end upon transcriptional activation, implying Yta7 may regulate H3 cotranscriptionally.
authors.affiliation: Department of Molecular and Cell Biology, and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA.
authors.forename: Laura M
authors.initials: LM
authors.lastname: Lombardi
authors.forename: Aisha
authors.initials: A
authors.lastname: Ellahi
authors.forename: Jasper
authors.initials: J
authors.lastname: Rine
mesh_terms: D000251:Adenosine Triphosphatases / Q000235:genetics / Q000378:metabolism; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D002868:Chromosomal Proteins, Non-Histone / Q000235:genetics* / Q000378:metabolism; D004591:Electrophoresis, Polyacrylamide Gel; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D006657:Histones / Q000235:genetics / Q000378:metabolism; D006801:Humans; D009154:Mutation; D009707:Nucleosomes / Q000235:genetics* / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D011485:Protein Binding; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism
chemical_list: D002843:Chromatin; D002868:Chromosomal Proteins, Non-Histone; D006657:Histones; D009707:Nucleosomes; D029701:Saccharomyces cerevisiae Proteins; C508095:YTA7 protein, S cerevisiae; D000251:Adenosine Triphosphatases
references.citation: Cell. 2003 Nov 26;115(5):537-49
references.pmid: 14651846
references.citation: Mol Cell. 2007 Aug 3;27(3):393-405
references.pmid: 17679090
references.citation: Cell. 2005 Oct 21;123(2):219-31
references.pmid: 16239141
references.citation: EMBO Rep. 2005 Apr;6(4):354-60
references.pmid: 15776021
references.citation: Mol Syst Biol. 2010 Dec 21;6:448
references.pmid: 21179020
references.citation: EMBO J. 2004 Oct 27;23(21):4243-52
references.pmid: 15457216
references.citation: Cell. 2007 Feb 23;128(4):707-19
references.pmid: 17320508
references.citation: Mol Cell Biol. 2010 Nov;30(22):5260-72
references.pmid: 20855524
references.citation: PLoS Biol. 2011 Jun;9(6):e1001086
references.pmid: 21738444
references.citation: Mol Cell. 2009 Aug 14;35(3):365-76
references.pmid: 19683499
references.citation: Proc Natl Acad Sci U S A. 2007 Nov 13;104(46):18067-72
references.pmid: 17998543
references.citation: Science. 2010 Jan 22;327(5964):425-31
references.pmid: 20093466
references.citation: Cell Cycle. 2010 Oct 15;9(20):4236-44
references.pmid: 20948314
references.citation: Mol Biosyst. 2008 Nov;4(11):1085-93
references.pmid: 18931784
references.citation: Nat Struct Mol Biol. 2010 Feb;17(2):251-7
references.pmid: 20118936
references.citation: Nat Genet. 2009 Aug;41(8):941-5
references.pmid: 19633671
references.citation: Genes Dev. 2007 Jun 15;21(12):1519-29
references.pmid: 17575053
references.citation: Nat Rev Mol Cell Biol. 2005 Jul;6(7):519-29
references.pmid: 16072036
references.citation: Science. 2007 Mar 9;315(5817):1405-8
references.pmid: 17347438
references.citation: Methods. 2001 Jul;24(3):218-29
references.pmid: 11403571
references.citation: Annu Rev Genet. 2009;43:559-99
references.pmid: 19886812
references.citation: Yeast. 1998 Jul;14(10):953-61
references.pmid: 9717241
references.citation: Mol Cell. 2006 May 5;22(3):415-22
references.pmid: 16678113
references.citation: J Cell Biol. 2005 Apr 11;169(1):35-47
references.pmid: 15824130
references.citation: Cell. 1998 Jan 9;92(1):105-16
references.pmid: 9489704
references.citation: Nature. 2003 Oct 23;425(6960):859-64
references.pmid: 14574415
references.citation: Genes Dev. 2009 Jul 1;23(13):1522-33
references.pmid: 19515975
references.citation: Nature. 2009 Sep 10;461(7261):193-8
references.pmid: 19741699
references.citation: Curr Protoc Mol Biol. 2005 Feb;Chapter 21:Unit 21.3
references.pmid: 18265358
references.citation: Mol Cell. 2005 Mar 18;17(6):831-40
references.pmid: 15780939
references.citation: Curr Protoc Mol Biol. 2001 May;Chapter 13:Unit13.12
references.pmid: 18265096
references.citation: Dev Biol. 2010 Mar 15;339(2):258-66
references.pmid: 19527704
references.citation: J Mol Biol. 1992 Aug 20;226(4):1009-25
references.pmid: 1518041
references.citation: Mol Cell Biol. 2009 May;29(9):2346-58
references.pmid: 19273605
references.citation: Cell. 2000 Oct 27;103(3):411-22
references.pmid: 11081628
references.citation: Mol Cell Biol. 2009 Apr;29(7):1972-86
references.pmid: 19158270
references.citation: Cancer Res. 2009 Apr 15;69(8):3339-46
references.pmid: 19318566
references.citation: J Biol Chem. 2004 Dec 10;279(50):52069-74
references.pmid: 15452122
references.citation: Proc Natl Acad Sci U S A. 2010 Jun 22;107(25):11325-30
references.pmid: 20534568
references.citation: Mol Cell. 2007 Feb 9;25(3):345-55
references.pmid: 17289583
references.citation: Mol Cell. 2009 Aug 14;35(3):340-51
references.pmid: 19683497
references.citation: PLoS One. 2009 Aug 20;4(8):e6700
references.pmid: 19693276
references.citation: EMBO J. 2003 Apr 15;22(8):1846-56
references.pmid: 12682017
references.citation: Science. 2010 May 21;328(5981):1043-6
references.pmid: 20489023
references.citation: Nat Rev Genet. 2008 Jan;9(1):15-26
references.pmid: 18059368
references.citation: Nat Rev Mol Cell Biol. 2010 Apr;11(4):264-75
references.pmid: 20197778
references.citation: Cell. 1990 Jun 15;61(6):1089-101
references.pmid: 2190690
references.citation: PLoS Biol. 2010 Jun 22;8(6):e1000401
references.pmid: 20582323
references.citation: Cell. 1998 Nov 25;95(5):717-28
references.pmid: 9845373
references.citation: Mol Cell. 2002 Mar;9(3):541-52
references.pmid: 11931762
references.citation: Genetics. 2005 Nov;171(3):913-22
references.pmid: 16079223
references.citation: Methods Enzymol. 2006;411:134-93
references.pmid: 16939790
references.citation: Science. 2003 Aug 22;301(5636):1090-3
references.pmid: 12934006
references.citation: Nature. 1999 Nov 25;402(6760):418-21
references.pmid: 10586882
references.citation: Mol Cell Proteomics. 2005 Sep;4(9):1358-69
references.pmid: 15972895
references.citation: Mol Cell Biol. 1992 Nov;12(11):5249-59
references.pmid: 1406694
references.citation: Mol Cell Biol. 2009 Sep;29(17):4604-11
references.pmid: 19581291
references.citation: Mol Cell Biol. 2001 Sep;21(18):6270-9
references.pmid: 11509669
references.citation: Nat Cell Biol. 2009 Aug;11(8):925-33
references.pmid: 19578373
references.citation: Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5116-21
references.pmid: 11309499
references.citation: Mol Cell Proteomics. 2009 Apr;8(4):870-82
references.pmid: 19106085
references.citation: Cancer Res. 2010 Nov 15;70(22):9402-12
references.pmid: 20864510
references.citation: Annu Rev Biophys Biomol Struct. 2006;35:93-114
references.pmid: 16689629
references.citation: Yeast. 1999 Oct;15(14):1541-53
references.pmid: 10514571
references.citation: Proc Natl Acad Sci U S A. 2009 Sep 1;106(35):14926-31
references.pmid: 19706456
references.citation: Nature. 1997 Sep 18;389(6648):251-60
references.pmid: 9305837
references.citation: Mutat Res. 2007 May 1;618(1-2):116-29
references.pmid: 17313961
references.citation: Mol Cell. 2002 Jun;9(6):1191-200
references.pmid: 12086617
references.citation: Nat Genet. 2000 Dec;26(4):415-23
references.pmid: 11101837
references.citation: Genes Dev. 2005 Mar 15;19(6):677-82
references.pmid: 15769942
references.citation: Nat Rev Genet. 2009 Mar;10(3):161-72
references.pmid: 19204718
references.citation: Mol Cell Biol. 1987 Dec;7(12):4204-10
references.pmid: 3125420
references.citation: Cell. 2010 Jan 8;140(1):136-47
references.pmid: 20079334
references.citation: Genome Res. 2008 Jul;18(7):1073-83
references.pmid: 18550805
references.citation: Science. 1997 Oct 24;278(5338):680-6
references.pmid: 9381177
references.citation: Nature. 2007 Apr 12;446(7137):806-10
references.pmid: 17314980
references.citation: Genetics. 2008 May;179(1):291-304
references.pmid: 18493054
references.citation: Mol Cell Biol. 2004 Dec;24(23):10111-7
references.pmid: 15542822