Now you see it: Genome methylation makes a comeback in drosophila

BioEssays

Volumn 36, Issue 12, 2014, Pages 1138-1144

  Boffelli, Dario ^a   Takayama, Sachiko ^a   Martin, David I K ^a  

^a CHILDREN S HOSPITAL OAKLAND RESEARCH INSTITUTE   (United States)

Author keywords

Development; Drosophila; Methylation

Indexed keywords

5 METHYLCYTOSINE; DNA METHYLTRANSFERASE;

ARTICLE; CELL NUCLEUS; CPG ISLAND; DNA METHYLATION; DROSOPHILA MELANOGASTER; GENOMICS; METHYLATION; NONHUMAN; REGULATORY MECHANISM;

DROSOPHILA MELANOGASTER;

EID: 84920263936     PISSN: 02659247     EISSN: 15211878     Source Type: Journal    
DOI: 10.1002/bies.201400097     Document Type: Article

References (53)

1. Suzuki MM, Bird A. 2008. DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 9: 465-76.
2. Klose RJ, Bird AP. 2006. Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci 31: 89-97.
3. Bogdanović O, Veenstra GJC. 2009. DNA methylation and methyl-CpG binding proteins: developmental requirements and function. Chromosoma 118: 549-65.
4. Deaton AM, Bird A. 2011. CpG islands and the regulation of transcription. Genes Dev 25: 1010-22.
5. Bird AP, Wolffe AP. 1999. Methylation-induced repression - belts, braces, and chromatin. Cell 99: 451-4.
6. Smith ZD, Meissner A. 2013. DNA methylation: roles in mammalian development. Nat Rev Genet 14: 204-20.
7. Reddington JP, Pennings S, Meehan RR. 2013. Non-canonical functions of the DNA methylome in gene regulation. Biochem J 451: 13-23.
8. Zemach A, McDaniel IE, Silva P, Zilberman D. 2010. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328: 916-9.
9. Jones PA. 2012. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 13: 484-92.
10. Zilberman D. 2008. The evolving functions of DNA methylation. Curr Opin Plant Biol 11: 554-9.
11. Yoder JA, Walsh CP, Bestor TH. 1997. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet 13: 335-40.
12. Crichton JH, Dunican DS, Maclennan M, Meehan RR, et al. 2014. Defending the genome from the enemy within: mechanisms of retrotransposon suppression in the mouse germline. Cell Mol Life Sci 71: 1581-605.
13. Feinberg AP, Vogelstein B. 1983. Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301: 89-92.
14. Feng S, Jacobsen SE. 2011. Epigenetic modifications in plants: an evolutionary perspective. Curr Opin Plant Biol 14: 179-86.
15. Lister R, Pelizzola M, Dowen RH, Hawkins RD, et al. 2009. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462: 315-22.
16. Feng S, Cokus SJ, Zhang X, Chen P-Y, et al. 2010. Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci USA 107: 8689-94.
17. Stroud H, Do T, Du J, Zhong X, et al. 2014. Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nat Struct Mol Biol 21: 64-72.
18. Goll MG, Bestor TH. 2005. Eukaryotic cytosine methyltransferases. Annu Rev Biochem 74: 481-514.
19. Goll MG, Kirpekar F, Maggert KA, Yoder JA, et al. 2006. Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2. Science 311: 395-8.
20. Schaefer M, Pollex T, Hanna K, Tuorto F, et al. 2010. RNA methylation by Dnmt2 protects transfer RNAs against stress-induced cleavage. Genes Dev 24: 1590-5.
21. Li E, Bestor TH, Jaenisch R. 1992. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69: 915-26.
22. Okano M, Bell DW, Haber DA, Li E. 1999. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99: 247-57.
23. Klein CJ, Botuyan M-V, Wu Y, Ward CJ, et al. 2011. Mutations in DNMT1 cause hereditary sensory neuropathy with dementia and hearing loss. Nat Genet 43: 595-600.
24. Winkelmann J, Lin L, Schormair B, Kornum BR, et al. 2012. Mutations in DNMT1 cause autosomal dominant cerebellar ataxia, deafness and narcolepsy. Hum Mol Genet 21: 2205-10.
25. Tweedie S, Charlton J, Clark V, Bird A. 1997. Methylation of genomes and genes at the invertebrate-vertebrate boundary. Mol Cell Biol 17: 1469-75.
26. Urieli-Shoval S, Gruenbaum Y, Sedat J, Razin A. 1982. The absence of detectable methylated bases in Drosophila melanogaster DNA. FEBS Lett 146: 148-52.
27. Hung M-S, Karthikeyan N, Huang B, Koo H-C, et al. 1999. Drosophila proteins related to vertebrate DNA (5-cytosine) methyltransferases. Proc Natl Acad Sci USA 96: 11940-5.
28. Tweedie S, Ng H-H, Barlow AL, Turner BM, et al. 1999. Vestiges of a DNA methylation system in Drosophila melanogaster? Nat Genet 23: 389-90.
29. Lyko F, Ramsahoye BH, Jaenisch R. 2000. DNA methylation in Drosophila melanogaster. Nature 408: 538-40.
30. Gowher H, Leismann O, Jeltsch A. 2000. DNA of Drosophila melanogaster contains 5-methylcytosine. EMBO J 19: 6918-23.
31. Lyko F. 2001. DNA methylation learns to fly. Trends Genet 17: 169-72.
32. Kunert N, Marhold J, Stanke J, Stach D, et al. 2003. A Dnmt2-like protein mediates DNA methylation in Drosophila. Development 130: 5083-90.
33. Lyko F, Ramsahoye BH, Kashevsky H, Tudor M, et al. 1999. Mammalian (cytosine-5) methyltransferases cause genomic DNA methylation and lethality in Drosophila. Nat Genet 23: 363-6.
34. Marhold J, Kramer K, Kremmer E, Lyko F. 2004. The Drosophila MBD2/3 protein mediates interactions between the MI-2 chromatin complex and CpT/A-methylated DNA. Development 131: 6033-9.
35. Takayama S, Dhahbi J, Roberts A, Mao G, et al. 2014. Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity. Genome Res 24: 821-30.
36. Marhold J, Brehm A, Kramer K. 2004. The Drosophila methyl-DNA binding protein MBD2/3 interacts with the NuRD complex via p55 and MI-2. BMC Mol Biol 5: 20.
37. Graveley BR, Brooks AN, Carlson JW, Duff MO, et al. 2011. The developmental transcriptome of Drosophila melanogaster. Nature 471: 473-9.
38. Raja SJ, Charapitsa I, Conrad T, Vaquerizas JM, et al. 2010. The nonspecific lethal complex is a transcriptional regulator in Drosophila. Mol Cell 38: 827-41.
39. Dunwell TL, McGuffin LJ, Dunwell JM, Pfeifer GP. 2013. The mysterious presence of a 5-methylcytosine oxidase in the Drosophila genome: possible explanations. Cell Cycle 12: 3357-65.
40. Tahiliani M, Koh KP, Shen Y, Pastor WA, et al. 2009. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324: 930-5.
41. Ito S, Shen L, Dai Q, Wu SC, et al. 2011. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333: 1300-3.
42. Okano M, Xie S, Li E. 1998. Dnmt2 is not required for de novo and maintenance methylation of viral DNA in embryonic stem cells. Nucleic Acids Res 26: 2536-40.
43. Phalke S, Nickel O, Walluscheck D, Hortig F, et al. 2009. Retrotransposon silencing and telomere integrity in somatic cells of Drosophila depends on the cytosine-5 methyltransferase DNMT2. Nat Genet 41: 696-702.
44. Schaefer M, Lyko F. 2010. Lack of evidence for DNA methylation of Invader4 retroelements in Drosophila and implications for Dnmt2-mediated epigenetic regulation. Nat Genet 42: 920-1 author reply 1.
45. Phalke S, Nickel O, Reuter G. 2010. Reply to "Lack of evidence for DNA methylation of Invader4 retroelements in Drosophila and implications for Dnmt2-mediated epigenetic regulation". Nat Genet 42: 921.
46. Durdevic Z, Hanna K, Gold B, Pollex T, et al. 2013. Efficient RNA virus control in Drosophila requires the RNA methyltransferase Dnmt2. EMBO Rep 14: 269-75.
47. Raddatz G, Guzzardo PM, Olova N, Fantappie MR, et al. 2013. Dnmt2-dependent methylomes lack defined DNA methylation patterns. Proc Natl Acad Sci USA 110: 8627-31.
48. Capuano F, Mulleder M, Kok R, Blom HJ, et al. 2014. Cytosine DNA methylation is found in Drosophila melanogaster but absent in Saccharomyces cerevisiae, Schizosaccharomyces pombe, and other yeast species. Analyt Chem 86: 3697-702.
49. Jurkowski TP, Meusburger M, Phalke S, Helm M, et al. 2008. Human DNMT2 methylates tRNAAsp molecules using a DNA methyltransferase-like catalytic mechanism. RNA 14: 1663-70.
50. Warnecke PM, Stirzaker C, Song J, Grunau C, et al. 2002. Identification and resolution of artifacts in bisulfite sequencing. Methods 27: 101-7.
51. Flusberg BA, Webster DR, Lee JH, Travers KJ, et al. 2010. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Meth 7: 461-5.
52. Wallace EVB, Stoddart D, Heron AJ, Mikhailova E, et al. 2010. Identification of epigenetic DNA modifications with a protein nanopore. Chem Commun 46: 8195-7.
53. Bailey TL. 2011. DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics 27: 1653-9.