title: Prediction of nucleosome positioning based on transcription factor binding sites.
abstract: BACKGROUND
  The DNA of all eukaryotic organisms is packaged into nucleosomes, the basic repeating units of chromatin. The nucleosome consists of a histone octamer around which a DNA core is wrapped and the linker histone H1, which is associated with linker DNA. By altering the accessibility of DNA sequences, the nucleosome has profound effects on all DNA-dependent processes. Understanding the factors that influence nucleosome positioning is of great importance for the study of genomic control mechanisms. Transcription factors (TFs) have been suggested to play a role in nucleosome positioning in vivo.
  
  
  RESULTS
  Here, the minimum redundancy maximum relevance (mRMR) feature selection algorithm, the nearest neighbor algorithm (NNA), and the incremental feature selection (IFS) method were used to identify the most important TFs that either favor or inhibit nucleosome positioning by analyzing the numbers of transcription factor binding sites (TFBSs) in 53,021 nucleosomal DNA sequences and 50,299 linker DNA sequences. A total of nine important families of TFs were extracted from 35 families, and the overall prediction accuracy was 87.4% as evaluated by the jackknife cross-validation test.
  
  
  CONCLUSIONS
  Our results are consistent with the notion that TFs are more likely to bind linker DNA sequences than the sequences in the nucleosomes. In addition, our results imply that there may be some TFs that are important for nucleosome positioning but that play an insignificant role in discriminating nucleosome-forming DNA sequences from nucleosome-inhibiting DNA sequences. The hypothesis that TFs play a role in nucleosome positioning is, thus, confirmed by the results of this study.
authors.affiliation: The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.
authors.forename: Xianfu
authors.initials: X
authors.lastname: Yi
authors.forename: Yu-Dong
authors.initials: YD
authors.lastname: Cai
authors.forename: Zhisong
authors.initials: Z
authors.lastname: He
authors.forename: Weiren
authors.initials: W
authors.lastname: Cui
authors.forename: Xiangyin
authors.initials: X
authors.lastname: Kong
mesh_terms: D001665:Binding Sites; D042002:Chromatin Assembly and Disassembly; D009707:Nucleosomes / Q000235:genetics* / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
chemical_list: D009707:Nucleosomes; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors
references.citation: J Mol Biol. 1999 Oct 29;293(3):477-91
references.pmid: 10543944
references.citation: Cell. 1998 Jan 9;92(1):105-16
references.pmid: 9489704
references.citation: BMC Genomics. 2010 May 17;11:309
references.pmid: 20478020
references.citation: Nat Genet. 2004 Aug;36(8):900-5
references.pmid: 15247917
references.citation: FEBS J. 2007 May;274(9):2396-410
references.pmid: 17419736
references.citation: J Comput Chem. 2009 Jan 15;30(1):33-9
references.pmid: 18496789
references.citation: Curr Opin Cell Biol. 2007 Jun;19(3):250-6
references.pmid: 17466507
references.citation: PLoS One. 2010 Jun 03;5(6):e10933
references.pmid: 20532171
references.citation: Nature. 2007 Dec 13;450(7172):1031-5
references.pmid: 18075583
references.citation: Nature. 2009 Mar 19;458(7236):362-6
references.pmid: 19092803
references.citation: Biochem Biophys Res Commun. 2009 Jul 31;385(3):363-8
references.pmid: 19463783
references.citation: PLoS Comput Biol. 2008 Jan;4(1):e13
references.pmid: 18225943
references.citation: Cell. 2002 Feb 22;108(4):475-87
references.pmid: 11909519
references.citation: Mol Cell Biol. 2004 Nov;24(22):10026-35
references.pmid: 15509803
references.citation: Biochem Biophys Res Commun. 2006 Sep 29;348(3):1034-7
references.pmid: 16899225
references.citation: Mol Cell Biol. 2000 Mar;20(6):1899-910
references.pmid: 10688638
references.citation: Nature. 2007 Mar 29;446(7135):572-6
references.pmid: 17392789
references.citation: J Mol Biol. 2009 Mar 13;386(5):1411-22
references.pmid: 19070622
references.citation: J Mol Biol. 2007 Aug 17;371(3):649-68
references.pmid: 17586522
references.citation: EMBO J. 1991 Feb;10(2):361-8
references.pmid: 1899374
references.citation: Biophys J. 2008 Jun;94(12):4597-604
references.pmid: 18326654
references.citation: PLoS Comput Biol. 2007 Nov;3(11):e215
references.pmid: 17997593
references.citation: Bioinformatics. 2005 Jul 1;21(13):2933-42
references.pmid: 15860560
references.citation: Nat Genet. 2007 Oct;39(10):1235-44
references.pmid: 17873876
references.citation: Nucleic Acids Res. 2008 Nov;36(19):6228-36
references.pmid: 18829715
references.citation: Science. 2005 Jul 22;309(5734):626-30
references.pmid: 15961632
references.citation: Genome Biol. 2004;5(9):R62
references.pmid: 15345046
references.citation: Bioinformatics. 2008 Jun 15;24(12):1456-8
references.pmid: 18445607
references.citation: Mol Cell Biol. 1997 Aug;17(8):4397-405
references.pmid: 9234698
references.citation: J Biomol Struct Dyn. 2007 Aug;25(1):49-54
references.pmid: 17676937
references.citation: J Proteome Res. 2009 Feb;8(2):999-1003
references.pmid: 19099508
references.citation: Nature. 1999 Nov 25;402(6760):418-21
references.pmid: 10586882
references.citation: Genome Res. 2008 Jul;18(7):1084-91
references.pmid: 18448704
references.citation: J Biol Chem. 2001 Sep 14;276(37):35209-16
references.pmid: 11461917
references.citation: Crit Rev Biochem Mol Biol. 1995;30(4):275-349
references.pmid: 7587280
references.citation: Nat Genet. 2006 Oct;38(10):1210-5
references.pmid: 16964265
references.citation: PLoS Biol. 2008 Mar 18;6(3):e65
references.pmid: 18351804
references.citation: Nature. 2010 Jul 15;466(7304):388-92
references.pmid: 20512117
references.citation: Stat Appl Genet Mol Biol. 2008;7(1):Article14
references.pmid: 18454729
references.citation: PLoS Genet. 2008 Jul 25;4(7):e1000138
references.pmid: 18654629
references.citation: Mol Cell. 2006 Nov 3;24(3):469-79
references.pmid: 17081995
references.citation: Cell. 2008 May 16;133(4):716-26
references.pmid: 18485878
references.citation: Bioinformatics. 2007 Sep 15;23(18):2449-54
references.pmid: 17623704
references.citation: Nature. 2008 May 15;453(7193):358-62
references.pmid: 18408708
references.citation: Cell. 1999 Aug 6;98(3):285-94
references.pmid: 10458604
references.citation: IEEE Trans Pattern Anal Mach Intell. 2005 Aug;27(8):1226-38
references.pmid: 16119262
references.citation: Genome Res. 2007 Aug;17(8):1170-7
references.pmid: 17620451
references.citation: Chromosome Res. 2005;13(3):289-98
references.pmid: 15868422
references.citation: Genome Res. 2008 Jul;18(7):1073-83
references.pmid: 18550805
references.citation: Mol Cell. 2005 Jun 10;18(6):735-48
references.pmid: 15949447
references.citation: Nature. 2006 Aug 17;442(7104):772-8
references.pmid: 16862119