title: Quantifying the mechanisms for segmental duplications in mammalian genomes by statistical analysis and modeling.
abstract: A large number of the segmental duplications in mammalian genomes have been cataloged by genome-wide sequence analyses. The molecular mechanisms involved in these duplications mostly remain a matter of speculation. To uncover, test, and further quantify the hypotheses on the mechanisms for the recent duplications in the mammalian genomes, we have performed a series of statistical analyses on the sequences flanking the duplicated segments and proposed a dynamic model for the duplication process. The model, when applied to the human duplication data, indicates that approximately 30% of the recent human segmental duplications were caused by a recombination-like mechanism, among which 12% were mediated by the most recently active repeat, Alu. But a significant proportion of the duplications are caused by some mechanism independent of the repeat distribution. A less sure but similar picture is found in the rodent genomes. A further analysis on the physical features of the flanking sequences suggests that one of the uncharacterized duplication mechanisms shared by the mammalian genomes is surprisingly well correlated with the physical instability in the DNA sequences.
authors.affiliation: Department of Biology, New York University, New York, NY 10003, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhou
authors.forename: Bud
authors.initials: B
authors.lastname: Mishra
mesh_terms: D000818:Animals; D003627:Data Interpretation, Statistical; D019143:Evolution, Molecular; D020440:Gene Duplication; D023281:Genomics; D006801:Humans; D051379:Mice; D008957:Models, Genetic; D051381:Rats; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA
references.citation: Biochemistry. 1989 Sep 19;28(19):7842-9
references.pmid: 2611216
references.citation: Hum Mol Genet. 2003 Jun 1;12(11):1321-8
references.pmid: 12761047
references.citation: Proc Natl Acad Sci U S A. 1986 Jun;83(11):3746-50
references.pmid: 3459152
references.citation: Genome Biol. 2003;4(4):R25
references.pmid: 12702206
references.citation: Genome Res. 2004 Apr;14(4):493-506
references.pmid: 15059990
references.citation: Genes Chromosomes Cancer. 2002 Oct;35(2):97-112
references.pmid: 12203773
references.citation: Nature. 1998 Dec 17;396(6712):643-9
references.pmid: 9872311
references.citation: J Mol Evol. 1996 Jan;42(1):59-65
references.pmid: 8576965
references.citation: Genome Res. 2000 Nov;10(11):1726-36
references.pmid: 11076858
references.citation: Cancer Genet Cytogenet. 2002 Oct 15;138(2):149-52
references.pmid: 12505261
references.citation: Hum Mol Genet. 1997 Sep;6(9):1513-7
references.pmid: 9285788
references.citation: Genome Biol. 2003;4(8):R47
references.pmid: 12914656
references.citation: Proc Natl Acad Sci U S A. 1998 Jul 7;95(14):8141-6
references.pmid: 9653154
references.citation: Nature. 2004 Oct 21;431(7011):927-30
references.pmid: 15496912
references.citation: Science. 2002 Aug 9;297(5583):1003-7
references.pmid: 12169732
references.citation: Hum Mol Genet. 2003 Sep 1;12(17):2201-8
references.pmid: 12915466
references.citation: J Mol Biol. 1995 Feb 24;246(3):401-417
references.pmid: 7877164
references.citation: Genome Res. 2004 May;14(5):789-801
references.pmid: 15123579
references.citation: Proc Natl Acad Sci U S A. 1993 Apr 1;90(7):2999-3003
references.pmid: 8385354
references.citation: EMBO J. 2004 Jan 14;23(1):234-43
references.pmid: 14685272
references.citation: Nat Rev Genet. 2002 May;3(5):370-9
references.pmid: 11988762
references.citation: Nature. 2004 Apr 1;428(6982):493-521
references.pmid: 15057822
references.citation: Genome Res. 2003 Mar;13(3):358-68
references.pmid: 12618366
references.citation: Proc Natl Acad Sci U S A. 2003 Dec 9;100(25):14988-93
references.pmid: 14630947
references.citation: Genome Biol. 2004;5(4):R23
references.pmid: 15059256
references.citation: Genes Chromosomes Cancer. 2003 Nov;38(3):215-25
references.pmid: 14506695
references.citation: Nat Genet. 1999 Sep;23(1):41-6
references.pmid: 10471496
references.citation: Genome Res. 2003 Dec;13(12):2519-32
references.pmid: 14656960
references.citation: Am J Hum Genet. 2003 Oct;73(4):823-34
references.pmid: 14505274
references.citation: Virology. 2004 Oct 25;328(2):282-91
references.pmid: 15464848
references.citation: Mol Biol Evol. 2005 Jan;22(1):135-41
references.pmid: 15371527
references.citation: Nature. 2002 Dec 5;420(6915):520-62
references.pmid: 12466850