Evidence that Localized Variation in Primate Sequence Divergence Arises from an Influence of Nucleosome Placement on DNA Repair

Molecular Biology and Evolution

Volumn 27, Issue 3, 2010, Pages 637-649

  Ying, Hua ^a   Epps, Julian ^b   Williams, Rohan ^a   Huttley, Gavin ^a  

^a Biology and Environment   (Australia)

^b UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

5 methyl cytosine; Chromatin; Comparative genomics; CpG; Molecular evolution; Nucleosome; Substitution rate heterogeneity

Indexed keywords

5 METHYLCYTOSINE; DINUCLEOTIDE; DNA; SPACER DNA;

ARTICLE; CHROMATIN STRUCTURE; CONTROLLED STUDY; CORRELATION ANALYSIS; CPG ISLAND; DINUCLEOTIDE SUBSTITUTION; DNA DAMAGE; DNA REPAIR; EVOLUTIONARY RATE; GENE MUTATION; GENE SEQUENCE; GENETIC VARIABILITY; HUMAN; HUMAN CELL; INTRON; MOLECULAR EVOLUTION; MUTATION RATE; NONHUMAN; NUCLEOSOME; PHYLOGENY; PRIMATE; PROMOTER REGION; SCORING SYSTEM; SEQUENCE ALIGNMENT; STATISTICAL ANALYSIS; T LYMPHOCYTE;

CHI-SQUARE DISTRIBUTION; CHROMATIN; COMPUTATIONAL BIOLOGY; CPG ISLANDS; DEOXYRIBONUCLEASE I; DNA DAMAGE; DNA METHYLATION; DNA MUTATIONAL ANALYSIS; DNA REPAIR; EVOLUTION, MOLECULAR; FOURIER ANALYSIS; HUMANS; NUCLEOSOMES; PHYLOGENY; PROMOTER REGIONS, GENETIC; SIGNAL PROCESSING, COMPUTER-ASSISTED;

PRIMATES;

EID: 77249125310     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msp253     Document Type: Article

References (50)

1. Anastassiou D. 2001. Genomic signal processing. IEEE Signal Process Mag. 18(4):8-20.
2. Balhorn R, Weston S, Thomas C, Wyrobek AJ. 1984. DNA packaging in mouse spermatids. Synthesis of protamine variants and four transition proteins. Exp Cell Res. 150(2):298-308.
3. Birney E, Stamatoyannopoulos JA, Dutta A, et al. (310 co-authors). 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447(7146):799-816.
4. Bohr VA, Smith CA, Okumoto DS, Hanawalt PC. 1985. DNA repair in an active gene: removal of pyrimidine dimers from the DHFR gene of CHO cells is much more efficient than in the genome overall. Cell 40(2):359-369.
5. Boulikas T. 1992. Evolutionary consequences of nonrandom damage and repair of chromatin domains. J Mol Evol. 35(2):156-180.
6. Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE. 2008. High-resolution mapping and characterization of open chromatin across the genome. Cell 132(2):311-322.
7. Brown TC, Jiricny J. 1988. Different base/base mispairs are corrected with different efficiencies and specificities in monkey kidney cells. Cell 54:705-711.
8. Cheng KC, Cahill DS, Kasai H, Nishimura S, Loeb LA. 1992. 8-Hydroxyguanine, an abundant form of oxidative DNA damage, causes G-T and A-C substitutions. J Biol Chem. 267(1):166-172.
9. Cooper DN, Youssoufian H. 1988. The CpG dinucleotide and human genetic disease. Hum Genet. 78(2):151-155.
10. Dermitzakis ET, Clark AG. 2002. Evolution of transcription factor binding sites in mammalian gene regulatory regions: conservation and turnover. Mol Biol Evol. 19(7):1114-1121.
11. Elgin SC. 1981. DNAase I-hypersensitive sites of chromatin. Cell 27(3 Pt 2):413-415.
12. Eyre-Walker A. 1993. Recombination and mammalian genome evolution. Proc Biol Sci. 252(1335):237-243.
13. Eyre-Walker A, Hurst LD. 2001. The evolution of isochores. Nat Rev Genet. 2(7):549-555.
14. Felsenstein J. 2003. Inferring phylogenies. Sunderland (MA): Sinauer Associates.
15. Filatov DA, Gerrard DT. 2003. High mutation rates in human and ape pseudoautosomal genes. Gene 317(1-2):67-77
16. Green P, Ewing B, Miller W, Thomas PJ, Green ED. 2003. Transcription-associated mutational asymmetry in mammalian evolution. Nat Genet. 33(4):514-517.
17. Gross DS, Garrard WT. 1988. Nuclease hypersensitive sites in chro-matin. Annu Rev Biochem. 57:159-197.
18. Hasegawa M, Kishino H, Yano T. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 22(2):160-174.
19. Hoeijmakers JH. 2001. Genome maintenance mechanisms for preventing cancer. Nature 411(6835):366-374.
20. Holm S. 1979. A simple sequentially rejective multiple test procedure. Scand J Stat. 6(2):65-70.
21. Hubbard TJP, Aken BL, Ayling S, et al. (51 co-authors). 2009. Ensembl 2009. Nucleic Acids Res. 37(Database issue):D690-D697.
22. Jakobovits EB, Bratosin S, Aloni Y. 1980. A nucleosome-free region in SV40 minichromosomes. Nature 285(5762):263-265.
23. Karolchik D, Hinrichs AS, Kent WJ. 2007. The UCSC Genome Browser. Current protocols in bioinformatics. New York: John Wiley & Sons, Inc. Chapter 1, Unit 1.4.
24. Knight R, Maxwell P, Birmingham A, et al. (20 co-authors). 2007. PyCo-gent: a toolkit for making sense from sequence. Genome Biol. 8(8):R171.
25. Kunsch H. 1989. The jackknife and the bootstrap for general stationary observations. Ann Stat. 17:1217-1241.
26. Lindsay H, Yap VB, Ying H, Huttley GA. 2008. Pitfalls of the most commonly used models of context dependent substitution. Biol Direct. 3:52.
27. Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ. 1997. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389(6648):251-260.
28. Margulies EH, Cooper GM, Asimenos G, et al. (76 co-authors). 2007. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 17(6):760-774.
29. McGhee JD, Felsenfeld G. 1980. Nucleosome structure. Annu Rev Biochem. 49:1115-1156.
30. Mitchell-Olds T, James RV, Palmer MJ, Williams PH. 1995. Genetics of Brassica rapa (syn. campestris). 2. Multiple disease resistance to three fungal pathogens: Peronospora parasitica, Albugo candida and Leptosphaeria maculans. Heredity 75(Pt 4):362-369.
31. Ozsolak F, Song JS, Liu XS, Fisher DE. 2007. High-throughput mapping of the chromatin structure of human promoters. Nat Biotechnol. 25(2):244-248.
32. Prendergast JGD, Campbell H, Gilbert N, Dunlop MG, Bickmore WA, Semple CAM. 2007. Chromatin structure and evolution in the human genome. BMC Evol Biol. 7:72.
33. Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K. 2008. Dynamic regulation of nucleosome positioning in the human genome. Cell 132(5):887-898.
34. Segal E, Fondufe-Mittendorf Y, Chen L, Thastrom A, Field Y, Moore IK, Wang JZ, Widom J. 2006. A genomic code for nucleosome positioning. Nature 442(7104):772-778.
35. Shimada N, Matsudo H, Osano K, Arakawa H, Buerstedde JM, Matsumoto Y, Chayahara K, Torihata A, Ono M. 2006. Activation of the chicken Ig-beta locus by the collaboration of scattered regulatory regions through changes in chromatin structure. Nucleic Acids Res. 34(13):3794-3802.
36. Shiraishi M, Oates AJ, Sekiya T. 2002. An overview of the analysis of DNA methylation in mammalian genomes. Biol Chem. 383(6):893-906.
37. Siepel A, Bejerano G, Pedersen JS, et al. (15 co-authors). 2005. Evolu-tionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15(8):1034-1050.
38. Siepel A, Haussler D. 2004. Combining phylogenetic and hidden Markov models in biosequence analysis. J Comput Biol. 11(2-3):413-428.
39. Sinha NK, Haimes MD. 1981. Molecular mechanisms of substitution mutagenesis. An experimental test of the Watson-Crick and Topal-Fresco models of base mispairings. J Biol Chem. 256(20):10671-10683.
40. Steger DJ, Workman JL. 1997. Stable co-occupancy of transcription factors and histones at the HIV-1 enhancer. EMBO J. 16(9): 2463-2472.
41. Suter B, Thoma F. 2002. DNA-repair by photolyase reveals dynamic properties of nucleosome positioning in vivo. J Mol Biol. 319(2):395-406.
42. Topal MD, Fresco JR. 1976. Complementary base pairing and the origin of substitution mutations. Nature 263(5575):285-289.
43. Tretter SA. 1985. Estimating the frequency of a noisy sinusoid by linear regression. IEEE Trans Inf Theory. 31(6):832-835.
44. Vyas P, Vickers MA, Simmons DL, Ayyub H, Craddock CF, Higgs DR. 1992. Cis-acting sequences regulating expression of the human alpha-globin cluster lie within constitutively open chromatin. Cell 69(5):781-793.
45. Wakefield M, Maxwell P, Huttley G. 2005. Vestige: maximum likelihood phylogenetic footprinting. BMC Bioinformatics. 6(1):130.
46. Wakeley J. 1994. Substitution-rate variation among sites and the estimation of transition bias. Mol Biol Evol. 11(3):436-442.
47. Warnecke T, Batada NN, Hurst LD. 2008. The impact of the nucleo-some code on protein-coding sequence evolution in yeast. PLoS Genet. 4(11):e1000250.
48. Washietl S, Machne R, Goldman N. 2008. Evolutionary footprints of nucleosome positions in yeast. Trends Genet. 24: 583-587.
49. Watson JD, Crick FH. 1953. Genetical implications of the structure of deoxyribonucleic acid. Nature 171(4361):964-967.
50. Wilson MD, Barbosa-Morais NL, Schmidt D, Conboy CM, Vanes L, Tybulewicz VLJ, Fisher EMC, Tavaré S, Odom DT. 2008. Species-specific transcription in mice carrying human chromosome 21. Science 322(5900):434-438.