High resolution methylome map of rat indicates role of intragenic DNA methylation in identification of coding region

PLoS ONE

Volumn 7, Issue 2, 2012, Pages

  Sati, Satish ^a   Tanwar, Vinay Singh ^a   Kumar, K Anand ^b   Patowary, Ashok ^a   Jain, Vaibhav ^a   Ghosh, Sourav ^a   Ahmad, Shadab ^a   Singh, Meghna ^a   Reddy, S Umakar ^c   Chandak, Giriraj Ratan ^c   Raghunath, Manchala ^b   Sivasubbu, Sridhar ^a   Chakraborty, Kausik ^a   Scaria, Vinod ^a   Sengupta, Shantanu ^a  

^a CSIR INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY   (India)

^b NATIONAL INSTITUTE OF NUTRITION   (India)

^c CENTRE FOR CELLULAR AND MOLECULAR BIOLOGY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RNA;

ADULT ANIMAL; ALTERNATIVE RNA SPLICING; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; EXON; GENE EXPRESSION; GENE MAPPING; HIGH RESOLUTION METHYLOME MAP; HIGH THROUGHPUT SEQUENCING; IMMUNOPRECIPITATION; INTRON; LIVER; NONHUMAN; PROMOTER REGION; RAT; REAL TIME POLYMERASE CHAIN REACTION; UNTRANSLATED REGION; ANIMAL; GENE EXPRESSION REGULATION; GENETICS; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; METABOLISM; OPEN READING FRAME; PROTEOMICS; WISTAR RAT;

MAMMALIA; RATTUS;

ANIMALS; CHROMATOGRAPHY, LIQUID; CPG ISLANDS; DNA; DNA METHYLATION; EXONS; GENE EXPRESSION REGULATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; IMMUNOPRECIPITATION; INTRONS; LIVER; OPEN READING FRAMES; PROMOTER REGIONS, GENETIC; PROTEOMICS; RATS; RATS, WISTAR; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 84857071275     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0031621     Document Type: Article

References (48)

1. Bernstein BE, Meissner A, Lander ES, (2007) The mammalian epigenome. Cell 128: 669-681.
2. Szyf M, (2007) The dynamic epigenome and its implications in toxicology. Toxicol Sci 100: 7-23.
3. Bird A, (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16: 6-21.
4. Kelly TK, De Carvalho DD, Jones PA, (2010) Epigenetic modifications as therapeutic targets. Nat Biotechnol 28: 1069-1078.
5. Petronis A, (2010) Epigenetics as a unifying principle in the aetiology of complex traits and diseases. Nature 465: 721-727.
6. Portela A, Esteller M, (2010) Epigenetic modifications and human disease. Nat Biotechnol 28: 1057-1068.
7. Sharma P, Kumar J, Garg G, Kumar A, Patowary A, et al. (2008) Detection of altered global DNA methylation in coronary artery disease patients. DNA Cell Biol 27: 357-365.
8. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, et al. (2008) A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol 26: 779-785.
9. Tomazou EM, Rakyan VK, Lefebvre G, Andrews R, Ellis P, et al. (2008) Generation of a genomic tiling array of the human major histocompatibility complex (MHC) and its application for DNA methylation analysis. BMC Med Genomics 1: 19.
10. Park PJ, (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10: 669-680.
11. Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, et al. (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol 28: 1097-1105.
12. Bock C, Reither S, Mikeska T, Paulsen M, Walter J, et al. (2005) BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics 21: 4067-4068.
13. Laird PW, (2010) Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet 11: 191-203.
14. Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, et al. (2010) Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 466: 253-257.
15. Jacob HJ, (1999) Functional Genomics and Rat Models. Genome Res 9: 1013-1016.
16. Acosta D, Suzuki M, Connolly D, Thompson RF, Fazzari MJ, et al. (2011) DNA methylation changes in murine breast adenocarcinomas allow the identification of candidate genes for human breast carcinogenesis. Mamm Genome 22: 249-259.
17. Rosenfeld CS, (2010) Animal models to study environmental epigenetics. Biol Reprod 82: 473-488.
18. Thompson RF, Fazzari MJ, Niu H, Barzilai N, Simmons RA, et al. (2010) Experimental intrauterine growth restriction induces alterations in DNA methylation and gene expression in pancreatic islets of rats. J Biol Chem 285: 15111-15118.
19. Feng S, Cokus SJ, Zhang X, Chen PY, Bostick M, et al. (2010) Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci U S A 107: 8689-8694.
20. Laurent L, Wong E, Li G, Huynh T, Tsirigos A, et al. (2010) Dynamic changes in the human methylome during differentiation. Genome Res 20: 320-331.
21. Li H, Ruan J, Durbin R, (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18: 1851-1858.
22. Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, et al. (2011) The UCSC Genome Browser database: update 2011. Nucleic Acids Res 39: D876-882.
23. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9: R137.
24. Chavez L, Jozefczuk J, Grimm C, Dietrich J, Timmermann B, et al. (2010) Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage. Genome Res 20: 1441-1450.
25. Bock C, Tomazou EM, Brinkman AB, Muller F, Simmer F, et al. (2010) Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol 28: 1106-1114.
26. Mandal PK, Kazazian HH Jr, (2008) SnapShot: Vertebrate transposons. Cell 135: 192-192 e191.
27. Straussman R, Nejman D, Roberts D, Steinfeld I, Blum B, et al. (2009) Developmental programming of CpG island methylation profiles in the human genome. Nat Struct Mol Biol 16: 564-571.
28. Yamada Y, Watanabe H, Miura F, Soejima H, Uchiyama M, et al. (2004) A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 21q. Genome Res 14: 247-266.
29. Backdahl L, Herberth M, Wilson G, Tate P, Campos LS, et al. (2009) Gene body methylation of the dimethylarginine dimethylamino-hydrolase 2 (Ddah2) gene is an epigenetic biomarker for neural stem cell differentiation. Epigenetics 4: 248-254.
30. Koul S, Houldsworth J, Mansukhani MM, Donadio A, McKiernan JM, et al. (2002) Characteristic promoter hypermethylation signatures in male germ cell tumors. Mol Cancer 1: 8.
31. Shen-Orr SS, Tibshirani R, Khatri P, Bodian DL, Staedtler F, et al. (2010) Cell type-specific gene expression differences in complex tissues. Nat Methods 7: 287-289.
32. Koscielny G, Le Texier V, Gopalakrishnan C, Kumanduri V, Riethoven JJ, et al. (2009) ASTD: The Alternative Splicing and Transcript Diversity database. Genomics 93: 213-220.
33. Feinberg AP, Tycko B, (2004) The history of cancer epigenetics. Nat Rev Cancer 4: 143-153.
34. Gordenin DA, Lobachev KS, Degtyareva NP, Malkova AL, Perkins E, et al. (1993) Inverted DNA repeats: a source of eukaryotic genomic instability. Mol Cell Biol 13: 5315-5322.
35. Esteller M, Almouzni G, (2005) How epigenetics integrates nuclear functions. Workshop on epigenetics and chromatin: transcriptional regulation and beyond. EMBO Rep 6: 624-628.
36. Walsh CP, Chaillet JR, Bestor TH, (1998) Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat Genet 20: 116-117.
37. Dion V, Wilson JH, (2009) Instability and chromatin structure of expanded trinucleotide repeats. Trends Genet 25: 288-297.
38. Wang Y, Liska F, Gosele C, Sedova L, Kren V, et al. (2010) A novel active endogenous retrovirus family contributes to genome variability in rat inbred strains. Genome Res 20: 19-27.
39. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462: 315-322.
40. Chodavarapu RK, Feng S, Bernatavichute YV, Chen PY, Stroud H, et al. (2010) Relationship between nucleosome positioning and DNA methylation. Nature 466: 388-392.
41. Pandya-Jones A, Black DL, (2009) Co-transcriptional splicing of constitutive and alternative exons. RNA 15: 1896-1908.
42. Schwartz S, Meshorer E, Ast G, (2009) Chromatin organization marks exon-intron structure. Nat Struct Mol Biol 16: 990-995.
43. Schwartz S, Ast G, (2010) Chromatin density and splicing destiny: on the cross-talk between chromatin structure and splicing. EMBO J 29: 1629-1636.
44. Choi JK, Bae JB, Lyu J, Kim TY, Kim YJ, (2009) Nucleosome deposition and DNA methylation at coding region boundaries. Genome Biol 10: R89.
45. Anastasiadou C, Malousi A, Maglaveras N, Kouidou S, (2011) Human epigenome data reveal increased CpG methylation in alternatively spliced sites and putative exonic splicing enhancers. DNA Cell Biol 30: 267-275.
46. Luco RF, Allo M, Schor IE, Kornblihtt AR, Misteli T, (2011) Epigenetics in alternative pre-mRNA splicing. Cell 144: 16-26.
47. Brodsky AS, Meyer CA, Swinburne IA, Hall G, Keenan BJ, et al. (2005) Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells. Genome Biol 6: R64.
48. Yadav AK, Bhardwaj G, Basak T, Kumar D, Ahmad S, et al. (2011) A systematic analysis of eluted fraction of plasma post immunoaffinity depletion: implications in biomarker discovery. PLoS One 6: e24442.