title: Long-range oscillation in a periodic DNA sequence motif may influence nucleosome array formation.
abstract: We have experimentally examined the characteristics of nucleosome array formation in different regions of mouse liver chromatin, and have computationally analyzed the corresponding genomic DNA sequences. We have shown that the mouse adenosine deaminase (MADA) gene locus is packaged into an exceptionally regular nucleosome array with a shortened repeat, consistent with our computational prediction based on the DNA sequence. A survey of the mouse genome indicates that <10% of 70 kb windows possess a nucleosome-ordering signal, consisting of regular long-range oscillations in the period-10 triplet motif non-T, A/T, G (VWG), which is as strong as the signal in the MADA locus. A strong signal in the center of this locus, confirmed by in vitro chromatin assembly experiments, appears to cooperate with weaker, in-phase signals throughout the locus. In contrast, the mouse odorant receptor (MOR) locus, which lacks locus-wide signals, was representative of approximately 40% of the mouse genomic DNA surveyed. Within this locus, nucleosome arrays were similar to those of bulk chromatin. Genomic DNA sequences which were computationally similar to MADA or MOR resulted in MADA- or MOR-like nucleosome ladders experimentally. Overall, we provide evidence that computationally predictable information in the DNA sequence may affect nucleosome array formation in animal tissue.
authors.affiliation: Department of Biological Sciences, Purdue University West Lafayette, IN 47907, USA.
authors.forename: Yamini
authors.initials: Y
authors.lastname: Dalal
authors.forename: Tomara J
authors.initials: TJ
authors.lastname: Fleury
authors.forename: Alfred
authors.initials: A
authors.lastname: Cioffi
authors.forename: Arnold
authors.initials: A
authors.lastname: Stein
mesh_terms: D000243:Adenosine Deaminase / Q000235:genetics; D000818:Animals; D002843:Chromatin / Q000378:metabolism; D019295:Computational Biology; D004247:DNA / Q000737:chemistry*; D008099:Liver / Q000737:chemistry; D051379:Mice; D009707:Nucleosomes / Q000737:chemistry*; D018035:Receptors, Odorant / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA
chemical_list: D002843:Chromatin; D009707:Nucleosomes; D018035:Receptors, Odorant; D004247:DNA; D000243:Adenosine Deaminase
references.citation: Nature. 2003 Apr 24;422(6934):835-47
references.pmid: 12695777
references.citation: Curr Top Dev Biol. 2003;53:115-38
references.pmid: 12509126
references.citation: Trends Genet. 2004 Jul;20(7):320-6
references.pmid: 15219397
references.citation: Proc Natl Acad Sci U S A. 1993 Oct 1;90(19):9021-5
references.pmid: 8415647
references.citation: Trends Cell Biol. 1995 Jul;5(7):272-7
references.pmid: 14732111
references.citation: Nat Rev Mol Cell Biol. 2002 Jun;3(6):422-9
references.pmid: 12042764
references.citation: Mol Cell Biol. 2001 Apr;21(8):2867-79
references.pmid: 11283265
references.citation: Genomics. 1990 Aug;7(4):476-85
references.pmid: 2387582
references.citation: Anal Biochem. 1983 Jul 1;132(1):6-13
references.pmid: 6312838
references.citation: Biochemistry. 2004 Jun 1;43(21):6709-22
references.pmid: 15157105
references.citation: J Mol Biol. 1997 Jul 25;270(4):559-73
references.pmid: 9245587
references.citation: Nucleic Acids Res. 1999 Feb 1;27(3):848-53
references.pmid: 9889282
references.citation: Nucleic Acids Res. 2002 Dec 1;30(23):5103-9
references.pmid: 12466533
references.citation: Nature. 2002 Dec 5;420(6915):520-62
references.pmid: 12466850
references.citation: Somat Cell Mol Genet. 1996 Jul;22(4):261-78
references.pmid: 9000171
references.citation: J Biol Chem. 1995 Apr 14;270(15):8373-6
references.pmid: 7721727
references.citation: J Mol Biol. 1984 Sep 15;178(2):341-63
references.pmid: 6208368
references.citation: J Mol Biol. 1996 Nov 8;263(4):503-10
references.pmid: 8918932
references.citation: Biochem Biophys Res Commun. 1973 May 15;52(2):504-10
references.pmid: 4711166
references.citation: J Mol Biol. 1991 Dec 20;222(4):1131-47
references.pmid: 1662288
references.citation: Mol Cell Biol. 2003 Jul;23(13):4559-72
references.pmid: 12808097
references.citation: Cell. 1977 Apr;10(4):633-40
references.pmid: 862024
references.citation: Proc Natl Acad Sci U S A. 1994 Jun 7;91(12):5277-80
references.pmid: 8202481