The mutational spectrum of non-CpG DNA varies with CpG content

Genome Research

Volumn 20, Issue 7, 2010, Pages 875-882

  Walser, Jean Claude ^a,b   Furano, Anthony V ^a  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

^b UNIVERSITY OF BASEL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHIMPANZEE; CPG ISLAND; DNA SEQUENCE; GENE MUTATION; GENETIC CORRELATION; HUMAN; MUTATION RATE; MUTATIONAL ANALYSIS; NONHUMAN; ORTHOLOGY; PRIORITY JOURNAL;

ANIMALS; BASE COMPOSITION; BASE SEQUENCE; CPG ISLANDS; DNA; DNA MUTATIONAL ANALYSIS; GENETIC SPECIATION; HUMANS; LONG INTERSPERSED NUCLEOTIDE ELEMENTS; MAMMALS; MOLECULAR SEQUENCE DATA; MUTATION; PAN TROGLODYTES;

MAMMALIA; PAN;

EID: 77954027855     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.103283.109     Document Type: Article

References (67)

1. Andersen PL, Xu F, Xiao W. 2008. Eukaryotic DNA damage tolerance and translesion synthesis through covalent modifications of PCNA. Cell Res 18: 162-173.
2. Bielas JH, Loeb KR, Rubin BP, True LD, Loeb LA. 2006. Human cancers express a mutator phenotype. Proc Natl Acad Sci 103: 18238-18242.
3. Bird A. 2002. DNA methylation patterns and epigenetic memory. Genes Dev 16: 6-21.
4. Boissinot S, Chevret P, Furano AV. 2000. L1 (LINE-1) retrotransposon evolution and amplification in recent human history. Mol Biol Evol 17: 915-928. (Pubitemid 30346551)
5. Branscombe Miranda T, Jones PA. 2007. DNA methylation: The nuts and bolts of repression. J Cell Physiol 213: 384-390.
6. Bulmer M. 1986. Neighboring base effects on substitution rates in pseudogenes. Mol Biol Evol 3: 322-329. (Pubitemid 16063601)
7. Cedar H, Bergman Y. 2009. Linking DNA methylation and histone modification: Patterns and paradigms. Nat Rev Genet 10: 295-304.
8. Chimpanzee Sequencing Analysis Consortium. 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69-87.
9. Chuang LSH, Ian H-I, Koh T-W, Ng H-H, Xu G, Li BFL. 1997. Human DNA-(cytosine-5)methyltransferase-PCNA complex as a target for p21WAF1. Science 277: 1996-2000.
10. Coulondre C, Miller JH, Farabaugh PJ, Gilbert W. 1978.Molecular basis of base substitution hotspots in Escherichia coli. Nature 274: 775-780.
11. Duncan BK, Miller JH. 1980. Mutagenic deamination of cytosine residues in DNA. Nature 287: 560-561.
12. Duret L. 2009. Mutation patterns in the human genome: More variable than expected. PLoS Biol 7: e1000028. doi: 10.1371/journal.pbio.1000028.
13. Duret L, Galtier N. 2000. The covariation between TpA deficiency, CpG deficiency, and G+C content of human isochores is due to a mathematical artifact. Mol Biol Evol 17: 1620-1625.
14. Edgar RC. 2004. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
15. Ehrlich M, Wang RY. 1981. 5-Methylcytosine in eukaryotic DNA. Science 212: 1350-1357.
16. Ehrlich M, Gama-Sosa MA, Huang LH, Midgett RM, Kuo KC, McCune RA, Gehrke C. 1982. Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells. Nucleic Acids Res 10: 2709-2721.
17. Furano AV, Boissinot S. 2008. Long Interspersed Nuclear Elements (LINEs): Evolution. In Encyclopedia of Life Sciences (ELS). John Wiley, Chichester, UK. doi: 10.1002/9780470015902.a0005304.pub2.
18. Furano AV, Walser JC. 2009. Mutation rate of non-CpG DNA. In Encyclopedia of Life Sciences (ELS). John Wiley, Chichester, UK. doi: 10.1002/9780470015902. a0021740.
19. Gaffney DJ, Keightley PD. 2005. The scale of mutational variation in the murid genome. Genome Res 15: 1086-1094.
20. Gaffney DJ, Keightley PD. 2008. Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals. BMC Evol Biol 8: 265. doi: 10.1186/1471-2148-8-265.
21. Galtier N, Gouy M, Gautier C. 1996. SEAVIEW and PHYLO-WIN: Two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12: 543-548. (Pubitemid 27067449)
22. Giordano J, Ge Y, Gelfand Y, Abrusan G, Benson G, Warburton PE. 2007. Evolutionary history of mammalian transposons determined by genome-wide defragmentation. PLoS Comput Biol 3: e137. doi: 10.1371/journal.pcbi.0030137.
23. Green P, Ewing B, Miller W, Thomas PJ, Green ED. 2003. Transcription-associated mutational asymmetry in mammalian evolution. Nat Genet 33: 514-517.
24. Hardison RC, Roskin KM, Yang S, Diekhans M, Kent WJ,Weber R, Elnitski L, Li J, O'Connor M, Kolbe D, et al. 2003. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res 13: 13-26.
25. Harwood J, Tachibana A, Meuth M. 1991. Multiple dispersed spontaneous mutations: A novel pathway of mutation in a malignant human cell line. Mol Cell Biol 11: 3163-3170.
26. Hellmann I, Prufer K, Ji H, Zody MC, Paabo S, Ptak SE. 2005. Why do human diversity levels vary at a megabase scale? Genome Res 15: 1222-1231.
27. Hodgkinson A, Ladoukakis E, Eyre-Walker A. 2009. Cryptic variation in the human mutation rate. PLoS Biol 7: e1000027. doi: 10.1371/journal.pbio.1000027.
28. Hwang DG, Green P. 2004. Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc Natl Acad Sci 101: 13994-14001.
29. Indiani C, McInerney P, Georgescu R, Goodman MF, O'Donnell M. 2005. A sliding-clamp toolbelt binds high- and low-fidelity DNA polymerases simultaneously. Mol Cell Biol 19: 805-815.
30. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
31. Jaenisch R, Bird A. 2003. Epigenetic regulation of gene expression: How the genome integrates intrinsic and environmental signals. Nat Genet 33(Suppl): 245-254.
32. Jeong S, Liang G, Sharma S, Lin JC, Choi SH, Han H, Yoo CB, Egger G, Yang AS, Jones PA. 2009. Selective anchoring of DNA methyltransferases 3A and 3B to nucleosomes containing methylated DNA. Mol Cell Biol 29: 5366-5376.
33. Keightley PD, Gaffney DJ. 2003. Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents. Proc Natl Acad Sci 100: 13402-13406.
34. Khan H, Smit A, Boissinot S. 2006. Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. Genome Res 16: 78-87.
35. Khelifi A, Meunier J, Duret L, Mouchiroud D. 2006. GC content evolution of the human and mouse genomes: Insights from the study of processed pseudogenes in regions of different recombination rates. J Mol Evol 62: 745-752.
36. Kondrashov FA, Ogurtsov AY, Kondrashov AS. 2006. Selection in favor of nucleotidesGandCdiversifies evolutionrates and levels of polymorphism at mammalian synonymous sites. J Theor Biol 240: 616-626.
37. Krawczak M, Ball EV, Cooper DN. 1998. Neighboring-nucleotide effects on the rates of germ-line single-base-pair substitution in human genes. Am J Hum Genet 63: 474-488.
38. Lee K-y, Myung K. 2008. PCNA modifications for regulation of post-replication repair pathways. Mol Cells 26: 5-11.
39. Lees-Murdock DJ,Walsh CP. 2008. DNA methylation reprogramming in the germ line. Epigenetics 3: 5-13.
40. Lehmann AR, Niimi A, Ogi T, Brown S, Sabbioneda S, Wing JF, Kannouche PL, Green CM. 2007. Translesion synthesis: Y-family polymerases and the polymerase switch. DNA Repair 6: 891-899.
41. Li YQ, Zhou PZ, Zheng XD, Walsh CP, Xu GL. 2007. Association of Dnmt3a and thymine DNA glycosylase links DNA methylation with base-excision repair. Nucleic Acids Res 35: 390-400.
42. Liu S, Liu W, Jakubczak JL, Erexson GL, Tindall KR, Chan R, Muller WJ, Adhya S, Garges S, Merlino G. 2002. Genetic instability favoring transversions associated with ErbB2-induced mammary tumorigenesis. Proc Natl Acad Sci 99: 3770-3775.
43. Loeb LA, Monnat RJ. 2008. DNA polymerases and human disease. Nat Rev Genet 9: 594-604.
44. Martens JH, O'Sullivan RJ, Braunschweig U, Opravil S, Radolf M, Steinlein P, Jenuwein T. 2005. The profile of repeat-associated histone lysine methylation states in the mouse epigenome. EMBO J 24: 800-812.
45. McCulloch SD, Kunkel TA. 2008. The fidelity of DNA synthesis by eukaryotic replicative and translesion synthesis polymerases. Cell Res 18: 148-161.
46. Meunier J, Duret L. 2004. Recombination drives the evolution of GC-content in the human genome. Mol Biol Evol 21: 984-990.
47. Moldovan GL, Pfander B, Jentsch S. 2007. PCNA, the maestro of the replication fork. 129: 665-679.
48. Mugal CF, von Grunberg HH, Peifer M. 2009. Transcription-induced mutational strand bias and its effect on substitution rates in human genes. Mol Biol Evol 26: 131-142.
49. Nachman MW, Crowell SL. 2000. Estimate of the mutation rate per nucleotide in humans. Genetics 156: 297-304.
50. Nur I, Pascale E, Furano AV. 1988. The left end of rat L1 (L1Rn, long interspersed repeated) DNA which is a CpG island can function as a promoter. Nucleic Acids Res 16: 9233-9251.
51. Ochman H. 2003. Neutral mutations and neutral substitutions in bacterial genomes. Mol Biol Evol 20: 2091-2096.
52. Pennings S, Allan J, Davey CS. 2005. DNA methylation, nucleosome formation and positioning. Brief Funct Genomics Proteomics 3: 351-361.
53. Pfander B, Moldovan G-L, Sacher M, Hoege C, Jentsch S. 2005. SUMO-modified PCNA recruits Srs2 to prevent recombination during S phase. Nature 436: 428-433.
54. Prendergast JG, Campbell H, Gilbert N, Dunlop MG, Bickmore WA, Semple CA. 2007. Chromatin structure and evolution in the human genome. BMC Evol Biol 7: 72. doi: 10.1186/1471-2148-7-72.
55. R Development Core Team. 2007. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
56. Rice P, Longden I, Bleasby A. 2000. EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet 16: 276-277.
57. Sassaman DM, Dombroski BA, Moran JV, Kimberland ML, Naas TP, DeBerardinis RJ, Gabriel A, Swergold GD, Kazazian HH Jr. 1997. Many human L1 elements are capable of retrotransposition. Nat Genet 16: 37-43. (Pubitemid 27198154)
58. Seidman MM, Bredberg A, Seetharam S, Kraemer KH. 1987. Multiple point mutations in a shuttle vector propagated in human cells: Evidence for an error-prone DNA polymerase activity. Proc Natl Acad Sci 84: 4944-4948.
59. Stelter P, Ulrich HD. 2003. Control of spontaneous and damage-induced mutagenesis by SUMO and ubiquitin conjugation. Nature 425: 188-191.
60. Sved J, Bird A. 1990. The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model. Proc Natl Acad Sci 87: 4692-4696.
61. Taylor J, Tyekucheva S, Zody M, Chiaromonte F, Makova KD. 2006. Strong and weak male mutation bias at different sites in the primate genomes: Insights from the human-chimpanzee comparison. Mol Biol Evol 23: 565-573.
62. Teng G, Papavasiliou FN. 2007. Immunoglobulin somatic hypermutation. Annu Rev Genet 41: 107-120.
63. Tyekucheva S, Makova KD, Karro JE, Hardison RC, Miller W, Chiaromonte F. 2008. Human-macaque comparisons illuminate variation in neutral substitution rates. Genome Biol 9: R76. doi: 10.1186/gb-2008-9-4-r76.
64. Venkatesan RN, Bielas JH, Loeb LA. 2006. Generation of mutator mutants during carcinogenesis. DNA Repair 5: 294-302.
65. Walser JC, Ponger L, Furano AV. 2008. CpG dinucleotides and the mutation rate of non-CpG DNA. Genome Res 18: 1403-1414.
66. Walsh CP, Xu GL. 2006. Cytosine methylation and DNA repair. Curr Top Microbiol Immunol 301: 283-315.
67. Yoder JA,Walsh CP, Bestor TH. 1997. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet 13: 335-340.