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Epigenomics: Sequencing the Methylome

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Array Comparative Genomic Hybridization

Part of the book series: Methods in Molecular Biology ((MIMB,volume 973))

Abstract

DNA methylation patterns are increasingly surveyed through methods that utilize massively parallel sequencing. Sequence-based assays developed to detect DNA methylation can be broadly divided into those that depend on affinity enrichment, chemical conversion, or enzymatic restriction. The DNA fragments resulting from these methods are uniformly subjected to library construction and massively parallel sequencing. The sequence reads are subsequently aligned to a reference genome and subjected to specialized analytical tools to extract the underlying methylation signature. This chapter will outline these emerging techniques.

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References

  1. Fraga MF, Ballestar E, Paz MF et al (2005) Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci U S A 102(30):10604–10609

    Article  PubMed  CAS  Google Scholar 

  2. Humpherys D, Eggan K, Akutsu H et al (2001) Epigenetic instability in ES cells and cloned mice. Science 293(5527):95–97

    Article  PubMed  CAS  Google Scholar 

  3. Esteller M (2008) Epigenetics in cancer. N Engl J Med 358(11):1148–1159

    Article  PubMed  CAS  Google Scholar 

  4. Waddington C (1942) The pupil contraction as an epigenetic crisis in drosophila. Proc Zool Soc Lond A111(3–4):181–188

    Google Scholar 

  5. Waddington CH (1942) The epigenotype. Endeavour 1(1):18–20

    Google Scholar 

  6. Hirst M, Marra MA (2009) Epigenetics and human disease. Int J Biochem Cell Biol 41(1):136–146. doi:10.1016/j.biocel.2008.09.011

    Article  PubMed  CAS  Google Scholar 

  7. Baylin SB, Jones PA (2011) A decade of exploring the cancer epigenome—biological and translational implications. Nat Rev Cancer 11(10):726–734. doi:10.1038/nrc3130

    Article  PubMed  CAS  Google Scholar 

  8. Metzker ML (2010) Sequencing technologies—the next generation. Nat Rev Genet 11(1):31–46. doi:10.1038/nrg2626

    Article  PubMed  CAS  Google Scholar 

  9. Bamshad MJ, Ng SB, Bigham AW et al (2011) Exome sequencing as a tool for mendel­ian disease gene discovery. Nat Rev Genet 12(11):745–755. doi:10.1038/nrg3031

    Article  PubMed  CAS  Google Scholar 

  10. Meyerson M, Gabriel S, Getz G (2010) Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet 11(10):685–696. doi:10.1038/nrg2841

    Article  PubMed  CAS  Google Scholar 

  11. Hirst M, Marra MA (2011) Next generation sequencing based approaches to epigenomics. Brief Funct Genomic Proteomic 9(5–6):455–465. doi:10.1093/bfgp/elq035

    Google Scholar 

  12. Morozova O, Hirst M, Marra MA (2009) Applications of new sequencing technologies for transcriptome analysis. Annu Rev Genomics Hum Genet 10:135–151. doi:10.1146/annurev-genom-082908-145957

    Article  PubMed  CAS  Google Scholar 

  13. Barski A, Cuddapah S, Cui K et al (2007) High-resolution profiling of histone methylations in the human genome. Cell 129(4):823–837

    Article  PubMed  CAS  Google Scholar 

  14. Mortazavi A, Williams BA, Mccue K et al (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5(7):621–628. doi:10.1038/nmeth.1226

    Article  PubMed  CAS  Google Scholar 

  15. Bernstein BE, Stamatoyannopoulos JA, Costello JF et al (2010) The nih roadmap epigenomics mapping consortium. Nat Biotechnol 28(10):1045–1048. doi:10.1038/nbt1010-1045

    Article  PubMed  CAS  Google Scholar 

  16. Abbott A (2011) Europe to map the human epigenome. Nature 477(7366):518. doi:10.1038/477518a

    Article  PubMed  CAS  Google Scholar 

  17. Bird A (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16(1):6–21

    Article  PubMed  CAS  Google Scholar 

  18. Feinberg AP, Vogelstein B (1983) Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301(5895):89–92

    Article  PubMed  CAS  Google Scholar 

  19. Gama-Sosa MA, Slagel VA, Trewyn RW et al (1983) The 5-methylcytosine content of DNA from human tumors. Nucleic Acids Res 11(19):6883–6894

    Article  PubMed  CAS  Google Scholar 

  20. Lorsbach RB, Moore J, Mathew S et al (2003) TET1, a member of a novel protein family, is fused to MLL in acute myeloid leukemia containing the t(10;11)(q22;q23). Leukemia 17(3):637–641. doi:10.1038/sj.leu.2402834

    Article  PubMed  CAS  Google Scholar 

  21. Ito S, D’alessio AC, Taranova OV et al (2010) Role of tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 466(7310):1129–1133. doi:10.1038/nature09303

    Article  PubMed  CAS  Google Scholar 

  22. Koh KP, Yabuuchi A, Rao S et al (2011) Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells. Cell Stem Cell 8(2):200–213. doi:10.1016/j.stem.2011.01.008

    Article  PubMed  CAS  Google Scholar 

  23. Kriaucionis S, Heintz N (2009) The nuclear DNA base 5-hydroxymethylcytosine is present in purkinje neurons and the brain. Science 324(5929):929–930. doi:10.1126/science.1169786

    Article  PubMed  CAS  Google Scholar 

  24. Song CX, Szulwach KE, Fu Y et al (2011) Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotechnol 29(1):68–72. doi:10.1038/nbt.1732

    Article  PubMed  CAS  Google Scholar 

  25. Szwagierczak A, Bultmann S, Schmidt CS et al (2010) Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA. Nucleic Acids Res 38(19):e181. doi:10.1093/nar/gkq684

    Article  PubMed  CAS  Google Scholar 

  26. Tahiliani M, Koh KP, Shen Y et al (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by mll partner TET1. Science 324(5929):930–935. doi:10.1126/science.1170116

    Article  PubMed  CAS  Google Scholar 

  27. Penn NW, Suwalski R, O’riley C et al (1972) The presence of 5-hydroxymethylcytosine in animal deoxyribonucleic acid. Biochem J 126(4):781–790

    PubMed  CAS  Google Scholar 

  28. Ito S, Shen L, Dai Q et al (2011) Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333(6047):1300–1303. doi:10.1126/science.1210597

    Article  PubMed  CAS  Google Scholar 

  29. He YF, Li BZ, Li Z et al (2011) Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 333(6047):1303–1307. doi:10.1126/science.1210944

    Article  PubMed  CAS  Google Scholar 

  30. Wu H, Zhang Y (2011) Mechanisms and functions of tet protein-mediated 5-methylcytosine oxidation. Genes Dev 25(23):2436–2452. doi:10.1101/gad.179184.111

    Article  PubMed  CAS  Google Scholar 

  31. Cimmino L, Abdel-Wahab O, Levine RL et al (2011) Tet family proteins and their role in stem cell differentiation and transformation. Cell Stem Cell 9(3):193–204. doi:10.1016/j.stem.2011.08.007

    Article  PubMed  CAS  Google Scholar 

  32. Ehrlich M, Gama-Sosa MA, Huang LH et al (1982) Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells. Nucleic Acids Res 10(8):2709–2721

    Article  PubMed  CAS  Google Scholar 

  33. Yoder JA, Walsh CP, Bestor TH (1997) Cytosine methylation and the ecology of intragenomic parasites. Trends Genet 13(8):335–340

    Article  PubMed  CAS  Google Scholar 

  34. Irizarry RA, Ladd-Acosta C, Wen B et al (2009) The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 41(2):178–186. doi:10.1038/ng.298

    Article  PubMed  CAS  Google Scholar 

  35. Gardiner-Garden M, Frommer M (1987) CpG islands in vertebrate genomes. J Mol Biol 196(2):261–282

    Article  PubMed  CAS  Google Scholar 

  36. Meehan R, Lewis J, Cross S et al (1992) Transcriptional repression by methylation of CpG. J Cell Sci Suppl 16:9–14

    PubMed  CAS  Google Scholar 

  37. Lewis JD, Meehan RR, Henzel WJ et al (1992) Purification, sequence, and cellular localization of a novel chromosomal protein that binds to methylated DNA. Cell 69(6): 905–914

    Article  PubMed  CAS  Google Scholar 

  38. Jones PL, Veenstra GJ, Wade PA et al (1998) Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat Genet 19(2):187–191

    Article  PubMed  CAS  Google Scholar 

  39. Lorincz MC, Dickerson DR, Schmitt M et al (2004) Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells. Nat Struct Mol Biol 11(11):1068–1075. doi:10.1038/nsmb840

    Article  PubMed  CAS  Google Scholar 

  40. Chodavarapu RK, Feng S, Bernatavichute YV et al (2010) Relationship between nucleosome positioning and DNA methylation. Nature 466(7304):388–392. doi:10.1038/nature09147

    Article  PubMed  CAS  Google Scholar 

  41. Maunakea AK, Nagarajan RP, Bilenky M et al (2010) Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 466(7303):253–257. doi:10.1038/nature09165

    Article  PubMed  CAS  Google Scholar 

  42. Yasui DH, Peddada S, Bieda MC et al (2007) Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genes. Proc Natl Acad Sci U S A 104(49):19416–19421

    Article  PubMed  CAS  Google Scholar 

  43. Chahrour M, Jung SY, Shaw C et al (2008) MeCP2, a key contributor to neurological disease, activates and represses transcription. Science 320(5880):1224–1229

    Article  PubMed  CAS  Google Scholar 

  44. Antequera F, Bird A (1993) Number of CpG islands and genes in human and mouse. Proc Natl Acad Sci U S A 90(24):11995–11999

    Article  PubMed  CAS  Google Scholar 

  45. Robertson KD (2005) DNA methylation and human disease. Nat Rev Genet 6(8):597–610. doi:10.1038/nrg1655

    Article  PubMed  CAS  Google Scholar 

  46. Fraga MF, Herranz M, Espada J et al (2004) A mouse skin multistage carcinogenesis model reflects the aberrant DNA methylation patterns of human tumors. Cancer Res 64(16):5527–5534. doi:10.1158/0008-5472.CAN-03-4061

    Article  PubMed  CAS  Google Scholar 

  47. Esteller M (2008) Epigenetics in cancer. N Engl J Med 358(11):1148–1159. doi:10.1056/NEJMra072067

    Article  PubMed  CAS  Google Scholar 

  48. Weissmann S, Alpermann T, Grossmann V et al (2011) Landscape of TET2 mutations in acute myeloid leukemia. Leukemia. doi:10.1038/leu.2011.326

  49. Abdel-Wahab O, Mullally A, Hedvat C et al (2009) Genetic characterization of TET1, TET2, and TET3 alterations in myeloid malignancies. Blood 114(1):144–147. doi:10.1182/blood-2009-03-210039

    Article  PubMed  CAS  Google Scholar 

  50. Jankowska AM, Szpurka H, Tiu RV et al (2009) Loss of heterozygosity 4q24 and TET2 mutations associated with myelodysplastic/myeloproliferative neoplasms. Blood 113(25):6403–6410. doi:10.1182/blood-2009-02-205690

    Article  PubMed  CAS  Google Scholar 

  51. Yan H, Parsons DW, Jin G et al (2009) IDH1 and IDH2 mutations in gliomas. N Engl J Med 360(8):765–773. doi:10.1056/NEJMoa0808710

    Article  PubMed  CAS  Google Scholar 

  52. Parsons DW, Jones S, Zhang X et al (2008) An integrated genomic analysis of human glioblastoma multiforme. Science 321(5897):1807–1812. doi:10.1126/science.1164382

    Article  PubMed  CAS  Google Scholar 

  53. Mardis ER, Ding L, Dooling DJ et al (2009) Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med 361(11):1058–1066. doi:10.1056/NEJMoa0903840

    Article  PubMed  CAS  Google Scholar 

  54. Jacinto FV, Ballestar E, Ropero S et al (2007) Discovery of epigenetically silenced genes by methylated DNA immunoprecipitation in colon cancer cells. Cancer Res 67(24): 11481–11486. doi:10.1158/0008-5472.CAN-07-2687

    Article  PubMed  CAS  Google Scholar 

  55. Weber M, Hellmann I, Stadler MB et al (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39(4):457–466. doi:10.1038/ng1990

    Article  PubMed  CAS  Google Scholar 

  56. Weber M, Davies JJ, Wittig D et al (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37(8):853–862. doi:10.1038/ng1598

    Article  PubMed  CAS  Google Scholar 

  57. Ruike Y, Imanaka Y, Sato F et al (2010) Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing. BMC Genomics 11:137. doi:10.1186/1471-2164-11-137

    Article  PubMed  CAS  Google Scholar 

  58. Stroud H, Feng S, Morey Kinney S et al (2011) 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells. Genome Biol 12(6):R54. doi:10.1186/gb-2011-12-6-r54

    Article  PubMed  CAS  Google Scholar 

  59. Ficz G, Branco MR, Seisenberger S et al (2011) Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature 473(7347):398–402. doi:10.1038/nature10008

    Article  PubMed  CAS  Google Scholar 

  60. Wu H, D’alessio AC, Ito S et al (2011) Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells. Genes Dev 25(7):679–684. doi:10.1101/gad.2036011

    Article  PubMed  CAS  Google Scholar 

  61. Xu Y, Wu F, Tan L et al (2011) Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells. Mol Cell 42(4):451–464. doi:10.1016/j.molcel.2011.04.005

    Article  PubMed  CAS  Google Scholar 

  62. Szulwach KE, Li X, Li Y et al (2011) 5hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging. Nat Neurosci 14(12):1607–1616. doi:10.1038/nn.2959

    Article  PubMed  CAS  Google Scholar 

  63. Pastor WA, Pape UJ, Huang Y et al (2011) Genome-wide mapping of 5-hydroxy­methylcytosine in embryonic stem cells. Nature 473(7347):394–397. doi:10.1038/nature10102

    Article  PubMed  CAS  Google Scholar 

  64. Ko M, Huang Y, Jankowska AM et al (2010) Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature 468(7325):839–843. doi:10.1038/nature09586

    Article  PubMed  CAS  Google Scholar 

  65. Harris RA, Wang T, Coarfa C et al (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol 28(10):1097–1105. doi:10.1038/nbt.1682

    Article  PubMed  CAS  Google Scholar 

  66. Matarese F, Carrillo-De Santa Pau E, Stunnenberg HG (2011) 5-Hydroxymethyl­cytosine: a new kid on the epigenetic block? Mol Syst Biol 7:562. doi:10.1038/msb.2011.95

    Article  PubMed  Google Scholar 

  67. Serre D, Lee BH, Ting AH (2010) Mbd-isolated genome sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic Acids Res 38(2):391–399. doi:10.1093/nar/gkp992

    Article  PubMed  CAS  Google Scholar 

  68. Brinkman AB, Simmer F, Ma K et al (2010) Whole-genome DNA methylation profiling using MethylCap-seq. Methods 52(3):232–236. doi:10.1016/j.ymeth.2010.06.012

    Article  PubMed  CAS  Google Scholar 

  69. Nair SS, Coolen MW, Stirzaker C et al (2011) Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias. Epigenetics 6(1):34–44. doi:10.4161/epi.6.1.13313

    Article  PubMed  CAS  Google Scholar 

  70. Hayatsu H (2008) Discovery of bisulfite-mediated cytosine conversion to uracil, the key reaction for DNA methylation analysis–a personal account. Proc Jpn Acad Ser B Phys Biol Sci 84(8):321–330

    Article  PubMed  CAS  Google Scholar 

  71. Frommer M, Mcdonald LE, Millar DS et al (1992) A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci U S A 89(5):1827–1831

    Article  PubMed  CAS  Google Scholar 

  72. Lister R, O’malley RC, Tonti-Filippini J et al (2008) Highly integrated single-base resolution maps of the epigenome in arabidopsis. Cell 133(3):523–536. doi:10.1016/j.cell.2008.03.029

    Article  PubMed  CAS  Google Scholar 

  73. Lister R, Pelizzola M, Dowen RH et al (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462(7271):315–322. doi:10.1038/nature08514

    Article  PubMed  CAS  Google Scholar 

  74. Cokus SJ, Feng S, Zhang X et al (2008) Shotgun bisulphite sequencing of the arabidopsis genome reveals DNA methylation patterning. Nature 452(7184):215–219

    Article  PubMed  CAS  Google Scholar 

  75. Li Y, Zhu J, Tian G et al (2010) The DNA methylome of human peripheral blood mononuclear cells. PLoS Biol 8(11):e1000533. doi:10.1371/journal.pbio.1000533

    Article  PubMed  CAS  Google Scholar 

  76. Bormann Chung CA, Boyd VL, Mckernan KJ et al (2010) Whole methylome analysis by ultra-deep sequencing using two-base encoding. PLoS One 5(2):e9320. doi:10.1371/journal.pone.0009320

    Article  PubMed  CAS  Google Scholar 

  77. Laurent L, Wong E, Li G et al (2010) Dynamic changes in the human methylome during differentiation. Genome Res 20(3):320–331. doi:10.1101/gr.101907.109

    Article  PubMed  CAS  Google Scholar 

  78. Stadler MB, Murr R, Burger L et al (2011) DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480(7378):490–495. doi:10.1038/nature10716

    PubMed  CAS  Google Scholar 

  79. Birney E, Stamatoyannopoulos JA, Dutta A et al (2007) Identification and analysis of functional elements in 1% of the human genome by the encode pilot project. Nature 447(7146): 799–816. doi:10.1038/nature05874

    Article  PubMed  CAS  Google Scholar 

  80. Myers RM, Stamatoyannopoulos J, Snyder M et al (2011) A user’s guide to the encyclopedia of DNA elements (encode). PLoS Biol 9(4):e1001046. doi:10.1371/journal.pbio.1001046

    Article  CAS  Google Scholar 

  81. Ajay SS, Parker SC, Abaan HO et al (2011) Accurate and comprehensive sequencing of personal genomes. Genome Res 21(9):1498–1505. doi:10.1101/gr.123638.111

    Article  PubMed  Google Scholar 

  82. Huang Y, Pastor WA, Shen Y et al (2010) The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing. PLoS One 5(1):e8888. doi:10.1371/journal.pone.0008888

    Article  PubMed  CAS  Google Scholar 

  83. Hodges E, Smith AD, Kendall J et al (2009) High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Res 19(9):1593–1605. doi:10.1101/gr.095190.109

    Article  PubMed  CAS  Google Scholar 

  84. Lee EJ, Pei L, Srivastava G et al (2011) Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing. Nucleic Acids Res 39(19):e127. doi:10.1093/nar/gkr598

    Article  PubMed  CAS  Google Scholar 

  85. Taylor KH, Kramer RS, Davis JW et al (2007) Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Res 67(18):8511–8518. doi:10.1158/0008-5472.CAN-07-1016

    Article  PubMed  CAS  Google Scholar 

  86. Ball MP, Li JB, Gao Y et al (2009) Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol 27(4):361–368. doi:10.1038/nbt.1533

    Article  PubMed  CAS  Google Scholar 

  87. Meissner A, Gnirke A, Bell GW et al (2005) Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res 33(18):5868–5877. doi:10.1093/nar/gki901

    Article  PubMed  CAS  Google Scholar 

  88. Smith ZD, Gu H, Bock C et al (2009) High-throughput bisulfite sequencing in mammalian genomes. Methods 48(3):226–232. doi:10.1016/j.ymeth.2009.05.003

    Article  PubMed  CAS  Google Scholar 

  89. Gu H, Smith ZD, Bock C et al (2011) Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat Protoc 6(4):468–481. doi:10.1038/nprot.2010.190

    Article  PubMed  CAS  Google Scholar 

  90. Wang L, Sun J, Wu H et al (2012) Systematic assessment of reduced representation bisulfite sequencing to human blood samples: a promising method for large-sample-scale epigenomic studies. J Biotechnol 157(1):1–6. doi:10.1016/j.jbiotec.2011.06.034

    Article  PubMed  CAS  Google Scholar 

  91. Gu H, Bock C, Mikkelsen TS et al (2010) Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods 7(2):133–136. doi:10.1038/nmeth.1414

    Article  PubMed  CAS  Google Scholar 

  92. Wiegand KC, Shah SP, Al-Agha OM et al (2010) ARID1a mutations in endometriosis-associated ovarian carcinomas. N Engl J Med 363(16):1532–1543. doi:10.1056/NEJMoa1008433

    Article  PubMed  CAS  Google Scholar 

  93. Bock C, Tomazou EM, Brinkman AB et al (2010) Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol 28(10):1106–1114. doi:10.1038/nbt.1681

    Article  PubMed  CAS  Google Scholar 

  94. Deng J, Shoemaker R, Xie B et al (2009) Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat Biotechnol 27(4):353–360. doi:10.1038/nbt.1530

    Article  PubMed  CAS  Google Scholar 

  95. Hansen KD, Timp W, Bravo HC et al (2011) Increased methylation variation in epigenetic domains across cancer types. Nat Genet 43(8):768–775. doi:10.1038/ng.865

    Article  PubMed  CAS  Google Scholar 

  96. Bird AP, Taggart MH, Smith BA (1979) Methylated and unmethylated DNA compartments in the sea urchin genome. Cell 17(4):889–901

    Article  PubMed  CAS  Google Scholar 

  97. Colaneri A, Staffa N, Fargo DC et al (2011) Expanded methyl-sensitive cut counting reveals hypomethylation as an epigenetic state that highlights functional sequences of the genome. Proc Natl Acad Sci U S A 108(23):9715–9720. doi:10.1073/pnas.1105713108

    Article  PubMed  CAS  Google Scholar 

  98. Brunner AL, Johnson DS, Kim SW et al (2009) Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res 19(6):1044–1056. doi:10.1101/gr.088773.108

    Article  PubMed  CAS  Google Scholar 

  99. Oda M, Glass JL, Thompson RF et al (2009) High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers. Nucleic Acids Res 37(12):3829–3839. doi:10.1093/nar/gkp260

    Article  PubMed  CAS  Google Scholar 

  100. Flusberg BA, Webster DR, Lee JH et al (2010) Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods 7(6):461–465. doi:10.1038/nmeth.1459

    Article  PubMed  CAS  Google Scholar 

  101. Korlach J, Bjornson KP, Chaudhuri BP et al (2010) Real-time DNA sequencing from single polymerase molecules. Methods Enzymol 472:431–455. doi:10.1016/S0076-6879(10)72001-2

    Article  PubMed  CAS  Google Scholar 

  102. Eid J, Fehr A, Gray J et al (2009) Real-time DNA sequencing from single polymerase molecules. Science 323(5910):133–138. doi:10.1126/science.1162986

    Article  PubMed  CAS  Google Scholar 

  103. Clarke J, Wu H-C, Jayasinghe L et al (2009) Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nanotechnol 4(4):265–270. doi:10.1038/nnano.2009.12

    Article  PubMed  CAS  Google Scholar 

  104. The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing. Nature 467(7319):1061–1073. doi:10.1038/nature09534

    Google Scholar 

  105. Flicek P, Birney E (2009) Sense from sequence reads: methods for alignment and assembly. Nat Methods 6(11 Suppl):S6–S12. doi:10.1038/nmeth.1376

    Article  PubMed  CAS  Google Scholar 

  106. Li H, Durbin R (2009) Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics 25(14):1754–1760. doi:10.1093/bioinformatics/btp324

    Article  PubMed  CAS  Google Scholar 

  107. Langmead B, Trapnell C, Pop M et al (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10(3):R25. doi:10.1186/gb-2009-10-3-r25

    Article  PubMed  CAS  Google Scholar 

  108. Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map format and samtools. Bioinformatics 25(16):2078–2079. doi:10.1093/bioinformatics/btp352

    Article  PubMed  CAS  Google Scholar 

  109. Xi Y, Li W (2009) BSMAP: whole genome bisulfite sequence mapping program. BMC Bioinformatics 10:232. doi:10.1186/1471-2105-10-232

    Article  PubMed  CAS  Google Scholar 

  110. Coarfa C, Yu F, Miller CA et al (2010) Pash 3.0: a versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing. BMC Bioinformatics 11:572. doi:10.1186/1471-2105-11-572

    Article  PubMed  Google Scholar 

  111. Chen PY, Cokus SJ, Pellegrini M (2010) BS seeker: precise mapping for bisulfite sequencing. BMC Bioinformatics 11:203. doi:10.1186/1471-2105-11-203

    Article  PubMed  CAS  Google Scholar 

  112. Xi Y, Bock C, Muller F et al (2011) RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing. Bioinformatics. doi:10.1093/bioinformatics/btr668

  113. Krueger F, Andrews SR (2011) Bismark: a flexible aligner and methylation caller for bisulfite-Seq applications. Bioinformatics 27(11):1571–1572. doi:10.1093/bioinformatics/btr167

    Article  PubMed  CAS  Google Scholar 

  114. Dreszer TR, Karolchik D, Zweig AS et al (2012) The UCSC genome browser database: extensions and updates 2011. Nucleic Acids Res 40(Database issue):D918–D923. doi:10.1093/nar/gkr1055

    Article  PubMed  CAS  Google Scholar 

  115. Fejes AP, Robertson G, Bilenky M et al (2008) FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 24(15):1729–1730. doi:10.1093/bioinformatics/btn305

    Article  PubMed  CAS  Google Scholar 

  116. Nielsen CB, Cantor M, Dubchak I et al (2010) Visualizing genomes: techniques and challenges. Nat Methods 7(3 Suppl):S5–S15. doi:10.1038/nmeth.1422

    Article  PubMed  CAS  Google Scholar 

  117. Flicek P, Amode MR, Barrell D et al (2012) Ensemble 2012. Nucleic Acids Res 40(Database issue):D84–D90. doi:10.1093/nar/gkr991

    Article  PubMed  CAS  Google Scholar 

  118. Zhou X, Maricque B, Xie M et al (2011) The human epigenome browser at Washington University. Nat Methods 8(12):989–990. doi:10.1038/nmeth.1772

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

I would like to thank all of my colleagues in the field who have contributed the data discussed in this article and apologize to all those whose work has not been included because of space constraints. This work was supported by the US National Institutes of Health (NIH) Roadmap Epigenomics Program, NIH grant 5U01ES017154-02, and the Canadian Institutes of Health Research Grant 92093.

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Authors and Affiliations

  1. Department of Microbiology and Immunology, Centre for High-Throughput Biology, University of British Columbia, Vancouver, Canada

    Martin Hirst

  2. BC Cancer Agency, Canada’s Michael Smith Genome Sciences Centre, Vancouver, Canada

    Martin Hirst

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  1. Martin Hirst
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Correspondence to Martin Hirst .

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Editors and Affiliations

  1. , Dept. of Pathology & Lab. Medicine, The Ottawa Hospital, Smyth Road 501, Ottawa, K1H 8L6, Ontario, Canada

    Diponkar Banerjee

  2. , Dept. of Molecular Oncology, BC Cancer Agency, West 10th Avenue 675, Vancouver, V5T 4E6, British Columbia, Canada

    Sohrab P. Shah

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Hirst, M. (2013). Epigenomics: Sequencing the Methylome. In: Banerjee, D., Shah, S. (eds) Array Comparative Genomic Hybridization. Methods in Molecular Biology, vol 973. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-281-0_3

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  • DOI: https://doi.org/10.1007/978-1-62703-281-0_3

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-280-3

  • Online ISBN: 978-1-62703-281-0

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