title: Multiple sequence-specific factors generate the nucleosome-depleted region on CLN2 promoter.
abstract: Nucleosome-depleted regions (NDRs) are ubiquitous on eukaryotic promoters. The formation of many NDRs cannot be readily explained by previously proposed mechanisms. Here, we carry out a focused study on a physiologically important NDR in the yeast CLN2 promoter (CLN2pr). We show that this NDR does not result from intrinsically unfavorable histone-DNA interaction. Instead, we identified eight conserved factor binding sites, including that of Reb1, Mcm1, and Rsc3, that cause the local nucleosome depletion. These nucleosome-depleting factors (NDFs) work redundantly, and simultaneously mutating all their binding sites eliminates CLN2pr NDR. The loss of the NDR induces unreliable "on/off" expression in individual cell cycles, but in the presence of the NDR, NDFs have little direct effect on transcription. We present bioinformatic evidence that the formation of many NDRs across the genome involves multiple NDFs. Our findings also provide significant insight into the composition and spatial organization of functional promoters.
authors: Laboratory of Cell Cycle Genetics, The Rockefeller University, New York, NY, 10065, USA. lbai01@rockefeller.edu
authors: Lu
authors: L
authors: Bai
authors: Andrej
authors: A
authors: Ondracka
authors: Frederick R
authors: FR
authors: Cross
references: BMC Bioinformatics. 2009 Dec 22;10:442
references: 20028554
references: Genetics. 2003 Nov;165(3):1017-29
references: 14668361
references: Nature. 2007 Mar 29;446(7135):572-6
references: 17392789
references: Mol Cell Biol. 1994 Jul;14(7):4779-87
references: 8007977
references: Nature. 1981 Aug 13;292(5824):579-80
references: 7254354
references: J Cell Biochem. 2007 Oct 15;102(3):560-70
references: 17668451
references: Cancer Cell. 2007 Nov;12(5):432-44
references: 17996647
references: Nature. 2009 Mar 19;458(7236):362-6
references: 19092803
references: Genetics. 2005 Sep;171(1):49-61
references: 15965243
references: Yeast. 1993 Aug;9(8):847-57
references: 8212892
references: Genes Dev. 2002 Apr 1;16(7):806-19
references: 11937489
references: Nucleic Acids Res. 2000 Mar 15;28(6):1390-6
references: 10684934
references: Nucleic Acids Res. 2011 Mar;39(6):2032-44
references: 21081559
references: Curr Opin Genet Dev. 2002 Apr;12(2):243-8
references: 11893499
references: Nat Genet. 2009 Aug;41(8):941-5
references: 19633671
references: PLoS Biol. 2010 Jul 06;8(7):e1000414
references: 20625544
references: J Mol Biol. 1988 Nov 5;204(1):109-27
references: 3063825
references: Nature. 2008 Jul 17;454(7202):291-6
references: 18633409
references: EMBO J. 1995 Dec 1;14(23):5824-32
references: 8846775
references: Anal Biochem. 1991 Aug 15;197(1):83-90
references: 1952079
references: Science. 1993 Sep 17;261(5128):1551-7
references: 8372350
references: Mol Genet Genomics. 2001 Nov;266(3):374-84
references: 11713667
references: PLoS Comput Biol. 2010 Jan 22;6(1):e1000649
references: 20098497
references: Genes Dev. 1988 Feb;2(2):150-9
references: 2834270
references: Mol Cell. 2006 Jan 6;21(1):3-14
references: 16387649
references: PLoS One. 2008 Jan 23;3(1):e1468
references: 18213377
references: Nat Genet. 2007 Oct;39(10):1235-44
references: 17873876
references: Mol Cell Biol. 2004 Oct;24(20):9152-64
references: 15456886
references: Nucleic Acids Res. 1998 Sep 1;26(17):4056-62
references: 9705519
references: Nature. 2008 May 8;453(7192):246-50
references: 18418379
references: Curr Protoc Mol Biol. 2001 May;Chapter 21:Unit 21.6
references: 18265198
references: Proc Natl Acad Sci U S A. 2007 May 22;104(21):8833-8
references: 17502614
references: Science. 2005 Jul 22;309(5734):626-30
references: 15961632
references: Cell. 2008 Jul 11;134(1):74-84
references: 18614012
references: Genetics. 2006 Apr;172(4):2113-22
references: 16415362
references: Cell. 2010 Jan 8;140(1):99-110
references: 20085705
references: Science. 2006 May 19;312(5776):1054-9
references: 16709784
references: Yeast. 2000 Oct;16(14):1313-23
references: 11015728
references: Mol Cell. 2009 May 14;34(4):405-15
references: 19481521
references: Nucleic Acids Res. 2003 Jan 1;31(1):374-8
references: 12520026
references: Dev Cell. 2010 Apr 20;18(4):544-55
references: 20412770
references: EMBO J. 1995 Jun 1;14(11):2570-9
references: 7781610
references: Nat Struct Mol Biol. 2009 Aug;16(8):847-52
references: 19620965
references: Nucleic Acids Res. 1995 Sep 25;23(18):3786-7
references: 7479011
references: Cell. 2008 Mar 7;132(5):887-98
references: 18329373
references: Nature. 2000 Jan 20;403(6767):339-42
references: 10659857
references: Biochim Biophys Acta. 1994 Nov 22;1219(3):677-89
references: 7948025
references: Cell. 2010 Apr 30;141(3):407-18
references: 20434983
references: Genome Res. 2008 Jul;18(7):1084-91
references: 18448704
references: Nucleic Acids Res. 2008 Jan;36(Database issue):D132-6
references: 18032429
references: PLoS Biol. 2008 Mar 18;6(3):e65
references: 18351804
references: Mol Cell. 2008 Dec 26;32(6):878-87
references: 19111667
references: PLoS Comput Biol. 2008 Nov;4(11):e1000216
references: 18989395
references: Mol Cell Biol. 1994 Jul;14(7):4788-801
references: 8007978
references: Nature. 2008 May 15;453(7193):358-62
references: 18408708
references: Cell. 2005 Aug 26;122(4):517-27
references: 16122420
references: Cell. 2005 Oct 21;123(2):233-48
references: 16239142
references: Nat Rev Genet. 2009 Mar;10(3):161-72
references: 19204718
references: Genome Res. 2008 Jul;18(7):1073-83
references: 18550805
references: Cell. 2009 May 1;137(3):445-58
references: 19410542
references: Cell. 1997 Jul 11;90(1):145-55
references: 9230310
references: Mol Cell. 2005 Jun 10;18(6):735-48
references: 15949447
references: Nature. 2006 Aug 17;442(7104):772-8
references: 16862119
references: Mol Cell. 2004 Jun 4;14(5):657-66
references: 15175160
references: Nature. 2004 Sep 2;431(7004):99-104
references: 15343339
references: Curr Opin Cell Biol. 2002 Apr;14(2):140-8
references: 11891111