The genome of the stick insect Medauroidea extradentata is strongly methylated within genes and repetitive DNA

PLoS ONE

Volumn 4, Issue 9, 2009, Pages

  Krauss, Veiko ^a   Eisenhardt, Carina ^a   Unger, Tina ^a  

^a UNIVERSITY OF LEIPZIG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; DINUCLEOTIDE; DNA FRAGMENT; GENOMIC DNA; REPETITIVE DNA; 5 METHYLCYTOSINE; RESTRICTION ENDONUCLEASE;

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; CPG ISLAND; DEVELOPMENT; DNA METHYLATION; DNA SEQUENCE; EUKARYOTE; GENE SILENCING; GERM LINE; INSECT; INSECT GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; TRANSCRIPTION INITIATION; TRANSPOSON; VERTEBRATE; ANIMAL; BEE; CHEMISTRY; DROSOPHILA MELANOGASTER; GENETIC PROCEDURES; GENETIC TRANSCRIPTION; GENETICS; GENOME; GENOMICS; METABOLISM; NUCLEOTIDE REPEAT;

BACULUM EXTRADENTATUM; EUKARYOTA; HEXAPODA; PHASMATODEA; VERTEBRATA;

5-METHYLCYTOSINE; ANIMALS; BEES; CPG ISLANDS; CYTOSINE; DNA METHYLATION; DNA RESTRICTION ENZYMES; DROSOPHILA MELANOGASTER; GENE SILENCING; GENETIC TECHNIQUES; GENOME; GENOMICS; INSECTS; REPETITIVE SEQUENCES, NUCLEIC ACID; TRANSCRIPTION, GENETIC;

EID: 70349635324     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0007223     Document Type: Article

References (40)

1. Rein T, DePamphilis ML, Zorbas H (1998) Identifying 5-methylcytosine and related modifications in DNA genomes. Nucl Acids Res 27: 2255-2264.
2. Field LM, Lyko F, Mandrioli M, Prantera G (2004) DNA methylation in insects. Insect Mol Biol 13: 109-115.
3. Goll MG, Bestor TH (2005) Eukaryotic cytosine methyltransferases. Annu Rev Biochem 74: 481-514.
4. Colot V, Rossignol JL (1999) Eukaryotic DNA methylation as an evolutionary device. Bioessays 21: 402-411.
5. Yoder JA, Walsh CP, Bestor TH (1997) Cytosine methylation and the ecology of intragenomic parasites. Trends Genet 13: 335-340.
6. Walsh CP, Bestor TH (1999) Cytosine methylation and mammalian development. Genes Dev 13: 26-34.
7. Bird AP (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16: 6-21.
8. Regev A, Lamb MJ, Jablonka E (1998) The Role of DNA Methylation in Invertebrates: Developmental Regulation or Genome Defense? Mol Biol Evol 15: 880-891.
9. Simmen MW, Leitgeb S, Charlton J, Jones SJ, Harris BR, et al. (1999) Non-methylated transposable elements and methylated genes in a chordate genome. Science 283: 1164-1167.
10. Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S (2007) Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nature Genet 39: 61-69.
11. Phalke S, Nickel O, Walluscheck D, Hortig F, Onorati MC, 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.
12. Mandrioli M, Volpi N (2003) The genome of the lepidopteran Mamestra brassicae has a vertebrate-like content of methyl-cytosine. Genetica 119: 187-191.
13. Bird AP (1980) DNA methylation and the frequency of CpG in animal DNA. Nucl Acids Res 8: 1499-1504.
14. Mazin AL (2009) Suicidal function of DNA methylation in age-related genome disintegration. Ageing Res Rev;doi:10.1016/j.arr.2009.04.005.
15. Gregory TR (2009) Animal Genome Size Database. Available: http://www.genomesize.com. Accessed 2009 Aug 20.
16. Grimaldi D, Engel MS (2005) The evolution of the insects. New York: Cambridge University Press. 755 p.
17. Patel CV, Gopinathan KP (1987) Determination of trace amounts of 5-methylcytosine in DNA by reverse-phase high-performance liquid chromatography. Anal Biochem 164: 164-169.
18. Wang Y, Jorda M, Jones PL, Maleszka R, Ling X, et al. (2006) Functional CpG methylation system in a social insect. Science 314: 645-647.
19. REBASE. The Restriction Enzyme Database. Available: http://rebase.neb.com/rebase/rebase.html. Accessed 2009 Aug 20.
20. Simmen MW (2008) Genome-scale relationships between cytosine methylation and dinucleotide abundances in animals. Genomics 92: 33-40.
21. Whiting MF, Bradler S, Maxwell T (2003) Loss and recovery of wings in stick insects. Nature 421: 264-267.
22. Mandrioli M, Borsatti F (2007) Analysis of heterochromatic epigenetic markers in the holocentric chromosomes of the aphid Acyrthosiphon pisum. Chromosome Res 15: 1015-1022.
23. Tweedie S, Charlton, J Clark V Bird A (1997) Methylation of genomes and genes at the invertebrate-vertebrate boundary. Mol Cel Biol 17: 1469-1475.
24. Suzuki M, Bird A (2008) DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 9: 465-476.
25. Warnecke PM, Stirzaker C, Song J, Grunau C, Melki JR, et al. (2002) Identification and resolution of artifacts in bisulfite sequencing. Methods 27: 101-107.
26. Meissner A, Gnirke A, Bell GW, Ramsahoye BH, Lander ES, et al. (2005) Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucl Acids Res 33: 5868-5877.
27. Lyko F, Ramsahoye BH, Jaenisch R (2000) DNA methylation in Drosophila melanogaster. Nature 408: 538-540.
28. Deobagkar DN, Muralidharan K, Devare SG, Kalghatgi K, Chandra HS (1982) The mealybug chromosome system I: Unusual methylated bases and dinucleotides in DNA of Planococcus species. J Biosci 4: 513-526.
29. Mohan KN, Chandra HS (2005) Isolation and analysis of sequences showing sex-specific cytosine methylation in the mealybug Planococcus lilacinus. Mol Gen Genet 274: 557-568.
30. Ramsahoye BH, Biniszkiewicz D, Lyko F, Clark V, Bird AP, et al. (2000) Proc Natl Acad Sci USA 97: 5237-5242.
31. Grandjean V, Yaman R, Cuzin F, Rassoulzadegan M (2007) Inheritance of an epigenetic mark: the CpG DNA methyltransferase 1 is required for de novo establishment of a complex pattern of non-CpG methylation. PLoS ONE 2: e1136. Available: http://www.plosone.org/article/info:doi/10.1371/ journal.pone.0001136.
32. Bird AP (1995) Gene number, noise reduction and biological complexity. Trends Genet 11: 94-100.
33. Field LM (2000) Methylation and expression of amplified esterase genes in the aphid Myzus persicae (Sulzer). Biochem J 349: 863-868.
34. Hellman A, Chess A (2007) Gene body-specific methylation on the active X chromosome. Science 315: 1141-1143.
35. Ball MP, Li JB, Gao Y, Lee JH, LeProust EM, et al. (2009) Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol 27: 361-368.
36. Suzuki M, Kerr AR, De Sousa D, Bird A (2007) CpG methylation is targeted to transcription units in an invertebrate genome. Genome Res 17: 625-631.
37. Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, et al. (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126: 1189-1201.
38. Bongiorni S, Prantera G (2003) Imprinted facultative heterochromatization in mealybugs. Genetica 117: 271-279.
39. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14: 1188-1190.
40. Krauss V, Thümmler C, Georgi F, Lehmann J, Stadler PF, et al. (2008) Near intron positions are reliable phylogenetic markers: an application to holometabolous insects. Mol Biol Evol 25: 821-830.