title: Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae.
abstract: The exact lengths of linker DNAs connecting adjacent nucleosomes specify the intrinsic three-dimensional structures of eukaryotic chromatin fibers. Some studies suggest that linker DNA lengths preferentially occur at certain quantized values, differing one from another by integral multiples of the DNA helical repeat, approximately 10 bp; however, studies in the literature are inconsistent. Here, we investigate linker DNA length distributions in the yeast Saccharomyces cerevisiae genome, using two novel methods: a Fourier analysis of genomic dinucleotide periodicities adjacent to experimentally mapped nucleosomes and a duration hidden Markov model applied to experimentally defined dinucleosomes. Both methods reveal that linker DNA lengths in yeast are preferentially periodic at the DNA helical repeat ( approximately 10 bp), obeying the forms 10n+5 bp (integer n). This 10 bp periodicity implies an ordered superhelical intrinsic structure for the average chromatin fiber in yeast.
authors.affiliation: Department of Statistics, Northwestern University, Evanston, Illinois, United States of America. jzwang@northwestern.edu
authors.forename: Ji-Ping
authors.initials: JP
authors.lastname: Wang
authors.forename: Yvonne
authors.initials: Y
authors.lastname: Fondufe-Mittendorf
authors.forename: Liqun
authors.initials: L
authors.lastname: Xi
authors.forename: Guei-Feng
authors.initials: GF
authors.lastname: Tsai
authors.forename: Eran
authors.initials: E
authors.lastname: Segal
authors.forename: Jonathan
authors.initials: J
authors.lastname: Widom
mesh_terms: D002843:Chromatin / Q000737:chemistry / Q000235:genetics; D019295:Computational Biology; D004271:DNA, Fungal / Q000737:chemistry* / Q000235:genetics*; D005583:Fourier Analysis; D016681:Genome, Fungal; D008390:Markov Chains; D008957:Models, Genetic; D009707:Nucleosomes / Q000737:chemistry / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D016415:Sequence Alignment / Q000706:statistics & numerical data*
chemical_list: D002843:Chromatin; D004271:DNA, Fungal; D009707:Nucleosomes
references.citation: Nature. 2007 Mar 29;446(7135):572-6
references.pmid: 17392789
references.citation: Proc Natl Acad Sci U S A. 1979 Dec;76(12):6326-30
references.pmid: 392519
references.citation: Science. 2005 Jul 22;309(5734):626-30
references.pmid: 15961632
references.citation: J Biomol Struct Dyn. 2006 Apr;23(5):559-66
references.pmid: 16494506
references.citation: Proc Natl Acad Sci U S A. 1992 Feb 1;89(3):1095-9
references.pmid: 1736292
references.citation: Proc Natl Acad Sci U S A. 1998 Sep 15;95(19):11163-8
references.pmid: 9736707
references.citation: J Biomol Struct Dyn. 2005 Jun;22(6):687-94
references.pmid: 15842173
references.citation: FEBS Lett. 1976 Jul 15;66(2):274-80
references.pmid: 782917
references.citation: EMBO J. 1983;2(1):51-6
references.pmid: 11894908
references.citation: Nucleic Acids Res. 1981 Jun 25;9(12):2643-58
references.pmid: 7279658
references.citation: J Mol Biol. 1986 Oct 20;191(4):659-75
references.pmid: 3806678
references.citation: Biochemistry. 2004 Apr 27;43(16):4773-80
references.pmid: 15096046
references.citation: Proc Natl Acad Sci U S A. 2000 Jan 4;97(1):127-32
references.pmid: 10618382
references.citation: Q Rev Biophys. 2001 Aug;34(3):269-324
references.pmid: 11838235
references.citation: J Mol Biol. 2003 Sep 5;332(1):111-25
references.pmid: 12946351
references.citation: Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6506-11
references.pmid: 16617109
references.citation: Nature. 2005 Jul 7;436(7047):138-41
references.pmid: 16001076
references.citation: EMBO J. 1989 Jan;8(1):229-38
references.pmid: 2714251
references.citation: Nucleic Acids Res. 2005 Dec 09;33(21):6743-55
references.pmid: 16339114
references.citation: Nucleic Acids Res. 1982 Apr 10;10(7):2275-93
references.pmid: 6283474
references.citation: Curr Opin Struct Biol. 1998 Feb;8(1):33-40
references.pmid: 9519294
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Nature. 2006 Aug 17;442(7104):772-8
references.pmid: 16862119