Computational approaches for understanding the evolution of DNA methylation in animals

Epigenetics

Volumn 4, Issue 8, 2009, Pages 551-556

  Yi, Soojin V ^a   Goodisman, Michael A D ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Comparative genomics; DNA methylation; Imprinting; Mutation; Phenotypic plasticity

Indexed keywords

DNA METHYLTRANSFERASE;

DNA METHYLATION; EMPIRICAL RESEARCH; GENE SEQUENCE; GENETIC TRANSCRIPTION; GENOME; MOLECULAR EVOLUTION; NONHUMAN; REVIEW; SPECIES DIVERSITY;

ANIMALIA;

EID: 74549206356     PISSN: 15592294     EISSN: 15592308     Source Type: Journal    
DOI: 10.4161/epi.4.8.10345     Document Type: Review

References (64)

1. Bird A. Perceptions of epigenetics. Nature 2007; 447:396-8.
2. Goll MG, Bestor TH. Eukaryotic cytosine methyl-transferases. Annu Rev Biochem 2005; 74:481-514.
3. Hendrich B, Tweedie S. The methyl-CpG binding domain and the evolving role of DNA methylation in animals. Trends Genet 2003; 19:269-77.
4. Klose RJ, Bird AP. Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci 2006; 31:89-97.
5. Suzuki MM, Bird A. DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 2008; 9:465-76.
6. Field LM, Lyko F, Mandrioll M, Pranter G. DNA methylation in insects. Insect Mol Biol 2004; 13:109-15.
7. Suzuki MM, Bird A. DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 2008; 9:465-76.
8. Tweedie S, Charlton J, Clark V, Bird A. Methylation of genomes and genes at the invertebrate-vertebrate boundary. Mol Cell Biol 1997; 17:1469-75.
9. Mandrioli M, Volpi N. The genome of the lepidopteran Mamestra brassicae has a vertebrate-like content of methyl-cytosine. Genetica 2003; 119:187-91.
10. Kronforst MR, Gilley DC, Strassmann JE, Queller DC. DNA methylation is widespread across social hymenoptera. Curr Biol 2008; 18:287-8.
11. Fraga MF, Esteller M. DNA methylation: A profile of methods and applications. Biotechniques 2002; 33:632-49.
12. Shen L, Kondo Y, Guo Y, Zhang J, Zhang L, Ahmed S, et al. Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters. PLoS Genet 2007; 3:181.
13. Bock C, Lengauer T. Computational epigenetics. Bioinformatics 2008; 24:1-10.
14. Kumar S, Cheng X, Klimasauskas S, Mi S, Posfai K, Roberts RJ, et al. The DNA (cytosine-5) methyltransferases. Nuc Acids Research 1994; 22:1-10.
15. Hung M-S, Shen C-KJ. Eukaryotic methyl-CpG-binding domain proteins and chromatin modification. Eukaryotic Cell 2003; 2:841-6.
16. Colot V, Rossignol J-L. Eukaryotic DNA methylation as an evolutionary device. BioEssays 1999; 21:402-11.
17. Maleszka R. Epigenetic integration of environmental and genomic signals in honey bees. Epigenetics 2008; 3:188-92.
18. Jurkowski TP, Meusburger M, Phalke S, Helm M, Nellen W, Reuter G, et al. Human DNMT2 methylates tRNAAsp molecules using a DNA methyltransferase-like catalytic mechanism. RNA 2008; 14:1663-70.
19. Suzuki MM, Kerr ARW, De Sousa D, Bird A. CpG methylation is targeted to transcription units in an invertebrate genome. Genome Res 2007; 17:625-31.
20. Wang Y, Jorda M, Jones PL, Maleszka R, Ling X, Robertson HM, et al. Functional CpG methylation system in a social insect. Science 2006; 314:645-7.
21. Kucharski R, Maleszka J, Foret S, Maleszka R. Nutritional control of reproductive status in honeybees via DNA methylation. Science 2008; 319:1827-30.
22. Biology analysis group, Xia Q, Zhou Z, Lu C, Cheng D, Dai F, et al. A Draft Sequence for the Genome of the Domesticated Silkworm (Bombyx mori). Science 2004; 306:1937-40.
23. Uno T, Nomura Y, Nakamura M, Nakao A, Tajima S, Kanamaru K, et al. Expression, purification and characterization of methyl DNA binding protein from Bombyx mori. J Insect Sci 2005; 5:1-8.
24. Wade PA. Methyl CpG-binding proteins and transcriptional repression. BioEssays 2001; 23:1131-7.
25. Fatemi M, Wade PA. MBD family proteins: reading the epigenetic code. J Cell Sci 2006; 119:3033-7.
26. Nielsen R, Bustamante C, Clark AG, Glanowski S, Sackton TB, Hubisz MJ, et al. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol 2005; 3:170.
27. Nielsen R, Hellmann I, Hubisz MJ, Bustamante C, Clark AG. Recent and ongoing selection in the human genome. Nat Rev Genet 2007; 8:857-68.
28. Yang Z, Nielsen R. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol 2002; 19:908-17.
29. Coulondre C, Miller JH, Farabaugh PJ, Gilbert W. Molecular basis of base substitution hotspots in Escherichia coli. Nature 1978; 274:775-80.
30. Duncan BK, Miller JH. Mutagenic deamination of cytosine residues in DNA. Nature 1980; 287:560-1.
31. Bird AP, Taggart MH. Variable patterns of total DNA and rDNA methylation in animals. Nuc Acids Res 1980; 8:1485-97.
32. Bird A. DNA methylation and the frequency of CpG in animal DNA. Nuc Acids Res 1980; 8:1499-504.
33. Weber M, Hellmann I, Stadler MB, Ramos L, Pääbo S, Rebhan M, et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 2007; 39:457-66.
34. Antequera F, Bird A. Number of CpG islands and genes in the human and mouse. Proc Natl Acad Sci USA 1993; 90:11995-9.
35. Elango N, Yi S. DNA methylation and structural and functional bimodality of vertebrate promoters. Mol Biol Evol 2008; 25:1602-8.
36. Jiang C, Han L, Su B, Li W-H, Zhao Z. Features and trend of loss of promoter-associated CpG islands in the human and mouse genomes. Mol Biol Evol 2007; 24:1991-2000.
37. Fang F, Fan S, Zhang X, Zhang MQ. Predicting methylation status of CpG islands in the human brain. Bioinformatics 2006; 22:2204-9.
38. Das R, Dimitrova N, Xuan Z, Rollins RA, Haghighi F, Edwards JR, et al. Computational prediction of methylation status in human genomic sequences. Proc Natl Acad Sci USA 2006; 103:10713-6.
39. Takai D, Jones PA. Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci USA 2002; 99:3740-5.
40. Elango N, Hunt BH, Goodisman MAD, Yi S. DNA methylation is widespread and associated with differential gene expression in castes of the honeybee, Apis mellifera. Proc Natl Acad Sci USA 2009; 106:11206-11.
41. Wang Y, Leung FCC. In silico prediction of two classes of honeybee genes with CpG deficiency or CpG enrichment and sorting according to gene ontology classes. J Mol Evol 2009; 68:700-5.
42. Bird A. DNA methylation patterns and epigenetic memory. Genes & Development 2002; 16:6-21.
43. Mandrioli M. A new synthesis in epigenetics: towards a unified function of DNA methylation from invertebrates to vertebrates. Cell Mol Life Sci 2007; 64:2522-4.
44. Yoder JA, Walsh CP, Bestor TH. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet 1997; 13:335-40.
45. Elango N, Kim S-H, Program NCS, Vigoda E, Yi S. Mutations of different molecular origins exhibit contrasting patterns of regional substitution rate variation. PLoS Comp Biol 2008; 4:1000015.
46. Meunier J, Khelifi A, Navratil V, Duret L. Homology-dependent methylation in primate repetitive DNA. Proc Natl Acad Sci USA 2005; 102:5471-6.
47. Maksakova IA, Mager DL, Reiss D. Keeping active endogenous retroviral-like elements in check: the epigenetic perspective. Cell Mol Life Sci 2008; 65:3329-47.
48. Simmen MW, Leitgeb S, Charlton J, Jones SJ, Harris BR, Clark VH, et al. Nonmethylated Transposable Elements and Methylated Genes in a Chordate Genome. Science 1999; 283:1164-7.
49. Suzuki MM, Kerr ARW, De Sousa D, Bird A. CpG methylation is targeted to transcription units in an invertebrate genome. Genome Res 2007; 17:625-31.
50. Kucharski R, Maleszka J, Foret S, Maleszka R. Nutritional control of reproductive status in honey-bees via DNA methylation. Science 2008; 319:1827-30.
51. Moczek AP, Snell-Rood EC. The basis of bee-ing different: the role of gene silencing in plasticity. Evolution & Development 2008; 10:511-3.
52. Tycko B, Morison IM. Physiological functions of imprinted genes. J Cell Physiol 2002; 192:245-58.
53. Li E, Beard C, Jaenisch R. Role for DNA methylation in genomic imprinting. Nature 1993; 366:362-5.
54. Kronforst MR, Gilley DC, Strassmann JE, Queller DC. DNA methylation is widespread across social Hymenoptera. Curr Biol 2008; 18:287-8.
55. Schaefer M, Lyko F. DNA methylation with a sting: an active DNA methylation system in the honeybee. BioEssays 2007; 29:208-11.
56. Wild G, West SA. Genomic Imprinting and Sex Allocation. American Naturalist 2009; 173:1-14.
57. Queller DC. Theory of genomic imprinting conflict in social insects. BMC Evol Biol 2003; 3.
58. The Gene Ontology Consortium. Gene Ontology: tool for the unification of biology. Nat Genet 2000; 25:25-9.
59. Luedi PP, Dietrich FS, Weidman JR, Bosko JM, Jirtle RL, Hartemink AJ. Computational and experimental identification of novel human imprinted genes. Genome Res 2007; 17:1723-30.
60. Luedi PP, Hartemink AJ, Jirtle RL. Genome-wide prediction of imprinted murine genes. Genome Res 2005; 15:875-84.
61. Bird A. Gene number, noise reduction and biological complexity. Trends Genet 1995; 11:94-100.
62. Gutierrez A, Sommer RJ. Evolution of dnmt-2 and mbd-2-like genes in the free-living nematodes Pristionchus pacificus, Caenorhabditis elegans and Caenorhabditis briggsae. Nuc Acids Res 2004; 32:6388-96.
63. Albalat R. Evolution of DNA-methylation machinery: DNA methyltransferases and methyl-DNA binding proteins in the amphioxus Branchiostoma floridae. Develop Genes Evol 2008; 218:691-701.
64. Putnam NH, Butts T, Ferrier DEK, Furlong RF, Hellsten U, Kawashima T, et al. The amphioxus genome and the evolution of the chordate karyotype. Nature 2008; 453:1064-71.