Sequencing the cancer methylome

Methods in Molecular Biology

Volumn 1238, Issue , 2015, Pages 627-651

  Shull, Austin Y ^a   Noonepalle, Satish K ^a   Lee, Eun Joon ^a   Choi, Jeong Hyeon ^a   Shi, Huidong ^a  

^a NONE

Author keywords

5 Hydroxymethylation; Cancer; Epigenetics; Marker; Methylation; Methylome; Nextgeneration sequencing

Indexed keywords

5 HYDROXYMETHYLCYTOSINE; DNA BINDING PROTEIN; RESTRICTION ENDONUCLEASE;

ANALYTIC METHOD; ARTICLE; BIOINFORMATICS; CHROMATIN; DNA METHYLATION; DNA PURIFICATION; GENETIC ASSOCIATION; IMMUNOPRECIPITATION; NEOPLASM; NEXT GENERATION SEQUENCING; PRIORITY JOURNAL;

EID: 84921809529     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-1804-1_33     Document Type: Article

References (106)

1. Smith ZD, Meissner A (2013) DNA methylation: roles in mammalian development. Nat Rev Genet 14(3):204–220. doi: 10.1038/nrg3354
2. 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(3):247–257
3. Robertson KD (2005) DNA methylation and human disease. Nat Rev Genet 6(8):597–610. doi: 10.1038/nrg1655
4. Ito S, D’Alessio AC, Taranova OV, Hong K, Sowers LC, Zhang Y (2010) Role of Tet proteins in 5mC to 5hmC conversion, ES-cell selfrenewal and inner cell mass specifi cation. Nature 466(7310):1129–1133. doi: 10.1038/nature09303
5. 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
6. Tahiliani M, Koh KP, Shen YH, Pastor WA, Bandukwala H, Brudno Y, Agarwal S, Iyer LM, Liu DR, Aravind L, Rao A (2009) Conversion of 5-methylcytosine to 5- hydroxymethylcytosine in mammalian DNA by MLL partner TET 1. Science 324(5929):930–935. doi: 10.1126/science.1170116
7. He YF, Li BZ, Li Z, Liu P, Wang Y, Tang Q, Ding J, Jia Y, Chen Z, Li L, Sun Y, Li X, Dai Q, Song CX, Zhang K, He C, Xu GL (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
8. Ito S, Shen L, Dai Q, Wu SC, Collins LB, Swenberg JA, He C, Zhang Y (2011) Tet proteins can convert 5-methylcytosine to 5- formylcytosine and 5-carboxylcytosine. Science 333(6047):1300–1303. doi: 10.1126/science.1210597
9. Monk M, Boubelik M, Lehnert S (1987) Temporal and regional changes in DNA methylation in the embryonic, extraembryonic and germ cell lineages during mouse embryo development. Development 99(3):371–382
10. Koh KP, Yabuuchi A, Rao S, Huang Y, Cunniff K, Nardone J, Laiho A, Tahiliani M, Sommer CA, Mostoslavsky G, Lahesmaa R, Orkin SH, Rodig SJ, Daley GQ, Rao A (2011) Tet1 and Tet2 regulate 5- hydroxymethylcytosine production and cell lineage specifi cation in mouse embryonic stem cells. Cell Stem Cell 8(2): 200–213. doi: 10.1016/j.stem.2011.01.008
11. Gu TP, Guo F, Yang H, Wu HP, Xu GF, Liu W, Xie ZG, Shi L, He X, Jin SG, Iqbal K, Shi YG, Deng Z, Szabo PE, Pfeifer GP, Li J, Xu GL (2011) The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature 477(7366):606–610. doi: 10.1038/nature10443
12. Pastor WA, Aravind L, Rao A (2013) TETonic shift: biological roles of TET proteins in DNA demethylation and transcription. Nat Rev Mol Cell Biol 14(6):341–356. doi: 10.1038/nrm3589
13. 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
14. Lian CG, Xu Y, Ceol C, Wu F, Larson A, Dresser K, Xu W, Tan L, Hu Y, Zhan Q, Lee CW, Hu D, Lian BQ, Kleffel S, Yang Y, Neiswender J, Khorasani AJ, Fang R, Lezcano C, Duncan LM, Scolyer RA, Thompson JF, Kakavand H, Houvras Y, Zon LI, Mihm MC Jr, Kaiser UB, Schatton T, Woda BA, Murphy GF, Shi YG (2012) Loss of 5- hydroxymethylcytosine is an epigenetic hallmark of melanoma. Cell 150(6):1135–1146. doi: 10.1016/j.cell.2012.07.033
15. Callinan PA, Feinberg AP (2006) The emerging science of epigenomics. Hum Mol Genet 15(Suppl 1):R95–R101. doi: 10.1093/hmg/ddl095
16. Laird PW (2010) Principles and challenges of genome-wide DNA methylation analysis. Nat Rev Genet 11(3):191–203
17. Lister R, Ecker JR (2009) Finding the fi fth base: genome-wide sequencing of cytosine methylation. Genome Res 19(6):959–966. doi: 10.1101/gr.083451.108
18. Zilberman D, Henikoff S (2007) Genomewide analysis of DNA methylation patterns. Development 134(22):3959–3965. doi: 10.1242/dev.001131
19. Yan PS, Chen CM, Shi H, Rahmatpanah F, Wei SH, Caldwell CW, Huang TH (2001) Dissecting complex epigenetic alterations in breast cancer using CpG island microarrays. Cancer Res 61(23):8375–8380
20. Khulan B, Thompson RF, Ye K, Fazzari MJ, Suzuki M, Stasiek E, Figueroa ME, Glass JL, Chen Q, Montagna C, Hatchwell E, Selzer RR, Richmond TA, Green RD, Melnick A, Greally JM (2006) Comparative isoschizomer profi ling of cytosine methylation: the HELP assay. Genome Res 16(8):1046–1055. doi: 10.1101/gr.5273806
21. Estecio MR, Yan PS, Ibrahim AE, Tellez CS, Shen L, Huang TH, Issa JP (2007) Highthroughput methylation profi ling by MCA coupled to CpG island microarray. Genome Res 17(10):1529–1536. doi: 10.1101/gr.6417007
22. Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL, Schubeler D (2005) Chromosome-wide and promoter-specifi c analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37(8):853–862. http://www.nature.com/ng/journal/v37/n8/suppinfo/ng1598_S1.html
23. Rauch T, Li H, Wu X, Pfeifer GP (2006) MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifi es frequent methylation of homeodomain-containing genes in lung cancer cells. Cancer Res 66(16):7939–7947. doi: 10.1158/0008-5472.can-06-1888
24. Sandoval J, Heyn H, Moran S, Serra-Musach J, Pujana MA, Bibikova M, Esteller M (2011) Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome. Epigenetics 6(6):692–702
25. Michels KB, Binder AM, Dedeurwaerder S, Epstein CB, Greally JM, Gut I, Houseman EA, Izzi B, Kelsey KT, Meissner A, Milosavljevic A, Siegmund KD, Bock C, Irizarry RA (2013) Recommendations for the design and analysis of epigenome-wide association studies. Nat Methods 10(10):949–955. doi: 10.1038/nmeth.2632 .http://www.nature.com/nmeth/journal/v10/n10/abs/nmeth.2632.html#supplementary-information
26. Suzuki M, Jing Q, Lia D, Pascual M, McLellan A, Greally J (2010) Optimized design and data analysis of tag-based cytosine methylation assays. Genome Biol 11(4):R36
27. Challen GA, Sun D, Jeong M, Luo M, Jelinek J, Berg JS, Bock C, Vasanthakumar A, Gu H, Xi Y, Liang S, Lu Y, Darlington GJ, Meissner A, Issa J-PJ, Godley LA, Li W, Goodell MA (2012) Dnmt3a is essential for hematopoietic stem cell differentiation. Nat Genet 44(1):23–31. http://www.nature.com/ng/journal/v44/n1/abs/ng.1009.html#supplementary-information
28. Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O’Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF (2010) Comparison of sequencing-based methods to profi le DNA methylation and identifi cation of monoallelic epigenetic modifi cations. Nat Biotechnol 28(10):1097–1105. doi: 10.1038/nbt.1682
29. Choi JH, Li Y, Guo J, Pei L, Rauch TA, Kramer RS, Macmil SL, Wiley GB, Bennett LB, Schnabel JL, Taylor KH, Kim S, Xu D, Sreekumar A, Pfeifer GP, Roe BA, Caldwell CW, Bhalla KN, Shi H (2010) Genome-wide DNA methylation maps in follicular lymphoma cells determined by methylation- enriched bisulfi te sequencing. PLoS One 5(9):e13020. doi: 10.1371/journal.pone.0013020
30. Irizarry RA, Ladd-Acosta C, Carvalho B, Wu H, Brandenburg SA, Jeddeloh JA, Wen B, Feinberg AP (2008) Comprehensive highthroughput arrays for relative methylation (CHARM). Genome Res 18(5):780–790. doi: 10.1101/gr.7301508
31. Bhattacharyya S, Yu Y, Suzuki M, Campbell N, Mazdo J, Vasanthakumar A, Bhagat TD, Nischal S, Christopeit M, Parekh S, Steidl U, Godley L, Maitra A, Greally JM, Verma A (2013) Genome-wide hydroxymethylation tested using the HELP-GT assay shows redistribution in cancer. Nucleic Acids Res 41(16):e157. doi: 10.1093/nar/gkt601
32. Borgel J, Guibert S, Weber M (2012) Methylated DNA immunoprecipitation (MeDIP) from low amounts of cells. Methods Mol Biol 925:149–158. doi:10.1007/978-1-62703-011-3_9
33. Mohn F, Weber M, Schubeler D, Roloff TC (2009) Methylated DNA immunoprecipitation (MeDIP). Methods Mol Biol 507:55–64. doi: 10.1007/978-1-59745-522-0_5
34. Nair SS, Coolen MW, Stirzaker C, Song JZ, Statham AL, Strbenac D, Robinson MD, Clark SJ (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
35. Taiwo O, Wilson GA, Morris T, Seisenberger S, Reik W, Pearce D, Beck S, Butcher LM (2012) Methylome analysis using MeDIP-seq with low DNA concentrations. Nat Protoc 7(4):617–636. doi: 10.1038/nprot.2012.012
36. Vucic EA, Wilson IM, Campbell JM, Lam WL (2009) Methylation analysis by DNA immunoprecipitation (MeDIP). Methods Mol Biol 556: 141–153. doi: 10.1007/978-1-60327-192-9.10
37. Feber A, Wilson GA, Zhang L, Presneau N, Idowu B, Down TA, Rakyan VK, Noon LA, Lloyd AC, Stupka E, Schiza V, Teschendorff AE, Schroth GP, Flanagan A, Beck S (2011) Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors. Genome Res 21(4):515–524. doi: 10.1101/gr.109678.110
38. Rauch TA, Pfeifer GP (2009) The MIRA method for DNA methylation analysis. Methods Mol Biol 507:65–75. doi: 10.1007/978-1-59745-522-0.6
39. Jin B, Ernst J, Tiedemann RL, Xu H, Sureshchandra S, Kellis M, Dalton S, Liu C, Choi JH, Robertson KD (2012) Linking DNA methyltransferases to epigenetic marks and nucleosome structure genome-wide in human tumor cells. Cell Rep 2(5):1411–1424. doi: 10.1016/j.celrep.2012.10.017
40. Ficz G, Branco MR, Seisenberger S, Santos F, Krueger F, Hore TA, Marques CJ, Andrews S, Reik W (2011) Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature 473(7347): 398–402. doi: 10.1038/nature10008
41. Wu H, D’Alessio AC, Ito S, Wang Z, Cui K, Zhao K, Sun YE, Zhang Y (2011) Genomewide 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
42. Song CX, Szulwach KE, Fu Y, Dai Q, Yi C, Li X, Li Y, Chen CH, Zhang W, Jian X, Wang J, Zhang L, Looney TJ, Zhang B, Godley LA, Hicks LM, Lahn BT, Jin P, He C (2011) Selective chemical labeling reveals the genome-wide distribution of 5- hydroxymethylcytosine. Nat Biotechnol 29(1):68–72. doi: 10.1038/nbt.1732
43. Robertson AB, Dahl JA, Ougland R, Klungland A (2012) Pull-down of 5- hydroxymethylcytosine DNA using JBP1- coated magnetic beads. Nat Protoc 7(2):340–350. doi: 10.1038/nprot.2011.443
44. Thomson JP, Hunter JM, Nestor CE, Dunican DS, Terranova R, Moggs JG, Meehan RR (2013) Comparative analysis of affi nity-based 5-hydroxymethylation enrichment techniques. Nucleic Acids Res 41(22):e206. doi: 10.1093/nar/gkt1080
45. Laurent L, Wong E, Li G, Huynh T, Tsirigos A, Ong CT, Low HM, Sung KWK, Rigoutsos I, Loring J, Wei CL (2010) Dynamic changes in the human methylome during differentiation. Genome Res 20(3):320–331. doi: 10.1101/gr.101907.109
46. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz- Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462(7271):315–322. doi: 10.1038/nature08514
47. Li YR, Zhu JD, Tian G, Li N, Li QB, Ye MZ, Zheng HC, Yu JA, Wu HL, Sun JH, Zhang HY, Chen QA, Luo RB, Chen MF, He YH, Jin X, Zhang QH, Yu C, Zhou GY, Sun JF, Huang YB, Zheng HS, Cao HZ, Zhou XY, Guo SC, Hu XD, Li X, Kristiansen K, Bolund L, Xu JJ, Wang W, Yang HM, Wang JA, Li RQ, Beck S, Wang J, Zhang XQ (2010) The DNA methylome of human peripheral blood mononuclear cells. PLoS Biol 8(11). ARTN e1000533. doi: 10.1371/journal.pbio.1000533
48. Hodges E, Molaro A, Dos Santos CO, Thekkat P, Song Q, Uren PJ, Park J, Butler J, Rafi i S, McCombie WR, Smith AD, Hannon GJ (2011) Directional DNA methylation changes and complex intermediate states accompany lineage specifi city in the adult hematopoietic compartment. Mol Cell 44(1):17–28. doi: 10.1016/j.molcel.2011.08.026
49. Berman BP, Weisenberger DJ, Aman JF, Hinoue T, Ramjan Z, Liu YP, Noushmehr H, Lange CPE, van Dijk CM, Tollenaar RAEM, Van den Berg D, Laird PW (2012) Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet 44(1):40–U62. doi: 10.1038/Ng.969
50. Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, Valsesia A, Ye Z, Kuan S, Edsall LE, Camargo AA, Stevenson BJ, Ecker JR, Bafna V, Strausberg RL, Simpson AJ, Ren B (2012) Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res 22(2):246–258. doi: 10.1101/gr.125872.111
51. Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, Wen B, Wu H, Liu Y, Diep D, Briem E, Zhang K, Irizarry RA, Feinberg AP (2011) Increased methylation variation in epigenetic domains across cancer types. Nat Genet 43(8):768–U777. doi: 10.1038/Ng.865
52. Berman BP, Weisenberger DJ, Aman JF, Hinoue T, Ramjan Z, Liu Y, Noushmehr H, Lange CPE, van Dijk CM, Tollenaar RAEM, Van Den Berg D, Laird PW (2012) Regions of focal DNA hypermethylation and long- range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet 44(1):40–46. http://www.nature.com/ng/journal/v44/n1/abs/ng.969.html#supplementary-information
53. Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, Wen B, Wu H, Liu Y, Diep D, Briem E, Zhang K, Irizarry RA, Feinberg AP (2011) Increased methylation variation in epigenetic domains across cancer types. Nat Genet 43(8):768–775. http://www.nature.com/ng/journal/v43/n8/abs/ng.865.html#supplementaryinformation
54. Lee EJ, Luo J, Wilson JM, Shi H (2013) Analyzing the cancer methylome through targeted bisulfi te sequencing. Cancer Lett 340(2):171–178. doi: 10.1016/j.canlet.2012.10.040
55. Deng J, Shoemaker R, Xie B, Gore A, LeProust EM, Antosiewicz-Bourget J, Egli D, Maherali N, Park IH, Yu JY, Daley GQ, Eggan K, Hochedlinger K, Thomson J, Wang W, Gao Y, Zhang K (2009) Targeted bisulfi te sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat Biotechnol 27(4):353–360. doi: 10.1038/Nbt.1530
56. Ball MP, Li JB, Gao Y, Lee JH, LeProust EM, Park IH, Xie B, Daley GQ, Church GM (2009) Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells (vol 27, pg 361, 2009). Nat Biotechnol 27(5):485. doi: 10.1038/Nbt0509-485b
57. Porreca GJ, Zhang K, Li JB, Xie B, Austin D, Vassallo SL, LeProust EM, Peck BJ, Emig CJ, Dahl F, Gao Y, Church GM, Shendure J (2007) Multiplex amplifi cation of large sets of human exons. Nat Methods 4(11):931–936. doi: 10.1038/Nmeth1110
58. Hodges E, Smith AD, Kendall J, Xuan ZY, Ravi K, Rooks M, Zhang MQ, Ye K, Bhattacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks JB (2009) High defi nition profi ling of mammalian DNA methylation by array capture and single molecule bisulfi te sequencing. Genome Res 19(9):1593–1605. doi: 10.1101/gr.095190.109
59. Lee EJ, Pei L, Srivastava G, Joshi T, Kushwaha G, Choi JH, Robertson KD, Wang X, Colbourne JK, Zhang L, Schroth GP, Xu D, Zhang K, Shi H (2011) Targeted bisulfi te sequencing by solution hybrid selection and massively parallel sequencing. Nucleic Acids Res 39(19):e127. doi: 10.1093/nar/gkr598, gkr598 [pii]
60. Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, Brockman W, Fennell T, Giannoukos G, Fisher S, Russ C, Gabriel S, Jaffe DB, Lander ES, Nusbaum C (2009) Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 27(2):182–189. doi: 10.1038/nbt.1523
61. Harrow J, Denoeud F, Frankish A, Reymond A, Chen C-K, Chrast J, Lagarde J, Gilbert J, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis S, Guigo R (2006) GENCODE: producing a reference annotation for ENCODE. Genome Biol 7(Suppl 1):S4
62. Varley KE, Mitra RD (2010) Bisulfi te patch PCR enables multiplexed sequencing of promoter methylation across cancer samples. Genome Res 20(9):1279–1287. doi: 10.1101/gr.101212.109
63. Tewhey R, Warner JB, Nakano M, Libby B, Medkova M, David PH, Kotsopoulos SK, Samuels ML, Hutchison JB, Larson JW, Topol EJ, Weiner MP, Harismendy O, Olson J, Link DR, Frazer KA (2009) Microdroplet- based PCR enrichment for large-scale targeted sequencing. Nat Biotechnol 27(11):1025–U1094. doi: 10.1038/Nbt.1583
64. Komori HK, LaMere SA, Torkamani A, Hart GT, Kotsopoulos S, Warner J, Samuels ML, Olson J, Head SR, Ordoukhanian P, Lee PL, Link DR, Salomon DR (2011) Application of microdroplet PCR for large-scale targeted bisulfi te sequencing. Genome Res 21(10):1738–1745. doi: 10.1101/gr.116863.110
65. Meissner A, Gnirke A, Bell GW, Ramsahoye B, Lander ES, Jaenisch R (2005) Reduced representation bisulfi te sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res 33(18):5868–5877. doi: 10.1093/Nar/Gki901
66. Gu H, Bock C, Mikkelsen TS, Jager N, Smith ZD, Tomazou E, Gnirke A, Lander ES, Meissner A (2010) Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods 7(2):133–U169. doi: 10.1038/Nmeth.1414
67. Boyle P, Clement K, Gu HC, Smith ZD, Ziller M, Fostel JL, Holmes L, Meldrim J, Kelley F, Gnirke A, Meissner A (2012) Gel- free multiplexed reduced representation bisulfi te sequencing for large-scale DNA methylation profi ling. Genome Biol 13(10). Artn R92. doi: 10.1186/Gb-2012-13-10-R92
68. Schneider-Stock R, Diab-Assef M, Rohrbeck A, Foltzer-Jourdainne C, Boltze C, Hartig R, Schonfeld P, Roessner A, Gali-Muhtasib H (2005) 5-Aza-cytidine is a potent inhibitor of DNA methyltransferase 3a and induces apoptosis in HCT-116 colon cancer cells via Gadd45- and p53-dependent mechanisms. J Pharmacol Exp Ther 312(2): 525–536. doi: 10.1124/jpet.104.074195
69. Huang Y, Pastor WA, Shen Y, Tahiliani M, Liu DR, Rao A (2010) The behaviour of 5-hydroxymethylcytosine in bisulfi te sequencing. PLoS One 5(1):e8888. doi: 10.1371/journal.pone.0008888
70. Booth MJ, Branco MR, Ficz G, Oxley D, Krueger F, Reik W, Balasubramanian S (2012) Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science 336(6083):934–937. doi: 10.1126/science.1220671
71. Booth MJ, Ost TWB, Beraldi D, Bell NM, Branco MR, Reik W, Balasubramanian S (2013) Oxidative bisulfi te sequencing of 5-methylcytosine and 5- hydroxymethylcytosine. Nat Protoc 8(10):1841–1851. doi: 10.1038/nprot.2013.115
72. Yu M, Hon GC, Szulwach KE, Song CX, Zhang L, Kim A, Li XK, Dai Q, Shen Y, Park B, Min JH, Jin P, Ren B, He C (2012) Baseresolution analysis of 5- hydroxymethylcytosine in the mammalian genome. Cell 149(6):1368–1380. doi: 10.1016/j.cell.2012.04.027
73. Brinkman AB, Gu H, Bartels SJJ, Zhang Y, Matarese F, Simmer F, Marks H, Bock C, Gnirke A, Meissner A, Stunnenberg HG (2012) Sequential ChIP-bisulfi te sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res 22(6):1128–1138. doi: 10.1101/gr.133728.111
74. Statham AL, Robinson MD, Song JZ, Coolen MW, Stirzaker C, Clark SJ (2012) Bisulfi te sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modifi ed DNA. Genome Res 22(6):1120–1127. doi: 10.1101/gr.132076.111
75. Huang Y, Pastor WA, Zepeda-Martínez JA, Rao A (2012) The anti-CMS technique for genomewide mapping of 5- hydroxymethylcytosine. Nat Protoc 7(10):1897–1908
76. Pondugula S, Kladde MP (2008) Singlemolecule analysis of chromatin: changing the view of genomes one molecule at a time. J Cell Biochem 105(2):330–337. doi: 10.1002/jcb.21849
77. Kelly TK, Miranda TB, Liang G, Berman BP, Lin JC, Tanay A, Jones PA (2010) H2A.Z maintenance during mitosis reveals nucleosome shifting on mitotically silenced genes. Mol Cell 39(6):901–911. doi: 10.1016/j.molcel.2010.08.026.S1097-2765(10)00636-2 [pii]
78. Lin JC, Jeong S, Liang G, Takai D, Fatemi M, Tsai YC, Egger G, Gal-Yam EN, Jones PA (2007) Role of nucleosomal occupancy in the epigenetic silencing of the MLH1 CpG island. Cancer Cell 12(5):432–444. doi: 10.1016/j.ccr.2007.10.014.S1535-6108(07)00299-1. [pii]
79. Kelly TK, Liu Y, Lay FD, Liang G, Berman BP, Jones PA (2012) Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Res 22(12):2497–2506. doi: 10.1101/gr.143008.112
80. Nabilsi NH, Deleyrolle LP, Darst RP, Riva A, Reynolds BA, Kladde MP (2014) Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifi es epigenetic heterogeneity in neural stem cells and glioblastoma. Genome Res 24(2):329–339. doi: 10.1101/gr.161737.113
81. 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
82. Langmead B, Trapnell C, Pop M, Salzberg S (2009) Ultrafast and memory-effi cient alignment of short DNA sequences to the human genome. Genome Biol 10(3):R25
83. Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24(5):713–714. doi: 10.1093/bioinformatics/btn025
84. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Graf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Backdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJP, Durbin R, Tavare S, Beck S (2008) A Bayesian deconvolution strategy for immunoprecipitation- based DNA methylome analysis. Nat Biotechnol 26(7):779–785. http://www.nature.com/nbt/journal/v26/n7/suppinfo/nbt1414_S1.html
85. Lienhard M, Grimm C, Morkel M, Herwig R, Chavez L (2013) MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments. Bioinformatics. doi: 10.1093/bioinformatics/btt650
86. Lan X, Adams C, Landers M, Dudas M, Krissinger D, Marnellos G, Bonneville R, Xu M, Wang J, Huang THM, Meredith G, Jin VX (2011) High resolution detection and analysis of CpG dinucleotides methylation using MBDSeq technology. PLoS One 6(7):e22226. doi: 10.1371/journal.pone.0022226
87. Wilson G, Dhami P, Feber A, Cortazar D, Suzuki Y, Schulz R, Schar P, Beck S (2012) Resources for methylome analysis suitable for gene knockout studies of potential epigenome modifi ers. Gigascience 1(1):3
88. Huang J, Renault V, Sengenès J, Touleimat N, Michel S, Lathrop M, Tost J (2012) MeQA: a pipeline for MeDIP-seq data quality assessment and analysis. Bioinformatics 28(4):587–588. doi: 10.1093/bioinformatics/btr699
89. He J, Sun X, Shao X, Liang L, Xie H (2013) DMEAS: DNA methylation entropy analysis software. Bioinformatics 29(16):2044–2045. doi: 10.1093/bioinformatics/btt332
90. Hansen K, Langmead B, Irizarry R (2012) BSmooth: from whole genome bisulfi te sequencing reads to differentially methylated regions. Genome Biol 13(10):R83
91. Akalin A AMP for aligning ERRBS and RRBS reads. http://code.google.com/p/amp-errbs/
92. Akalin A, Kormaksson M, Li S, Garrett- Bakelman F, Figueroa M, Melnick A, Mason C (2012) methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profi les. Genome Biol 13(10):R87
93. Choi J-H BSpipe: a comprehensive pipeline for BS-seq. http://sourceforge.net/projects/bspipe/
94. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D (2002) The human genome browser at UCSC. Genome Res 12(6):996–1006. doi: 10.1101/gr.229102
95. Thorvaldsdóttir H, Robinson JT, Mesirov JP (2013) Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14(2):178–192. doi: 10.1093/bib/bbs017
96. Nicol JW, Helt GA, Blanchard SG, Raja A, Loraine AE (2009) The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics 25(20):2730–2731. doi: 10.1093/bioinformatics/btp472
97. Mi H, Lazareva-Ulitsky B, Loo R, Kejariwal A, Vandergriff J, Rabkin S, Guo N, Muruganujan A, Doremieux O, Campbell MJ, Kitano H, Thomas PD (2005) The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res 33(suppl 1):D284–D288. doi: 10.1093/nar/gki078
98. Huang DW, Sherman BT, Lempicki RA (2008) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4(1):44–57. http://www.nature.com/nprot/journal/v4/n1/suppinfo/nprot.2008.211_S1.html
99. Ingenuity Pathway Analysis. http://www.ingenuity.com
100. Ghoshal K, Datta J, Majumder S, Bai S, Kutay H, Motiwala T, Jacob ST (2005) 5-Azadeoxycytidine induces selective degradation of DNA methyltransferase 1 by a proteasomal pathway that requires the KEN box, bromoadjacent homology domain, and nuclear localization signal. Mol Cell Biol 25(11):4727–4741. doi: 10.1128/MCB.25.11.4727-4741.2005
101. Li F, Papworth M, Minczuk M, Rohde C, Zhang Y, Ragozin S, Jeltsch A (2007) Chimeric DNA methyltransferases target DNA methylation to specifi c DNA sequences and repress expression of target genes. Nucleic Acids Res 35(1):100–112. doi: 10.1093/nar/gkl1035
102. Siddique AN, Nunna S, Rajavelu A, Zhang Y, Jurkowska RZ, Reinhardt R, Rots MG, Ragozin S, Jurkowski TP, Jeltsch A (2013) Targeted methylation and gene silencing of VEGF-A in human cells by using a designed Dnmt3a-Dnmt3L single-chain fusion protein with increased DNA methylation activity. J Mol Biol 425(3):479–491. doi: 10.1016/j.jmb.2012.11.038
103. Chen H, Kazemier HG, de Groote ML, Ruiters MH, Xu GL, Rots MG (2014) Induced DNA demethylation by targeting Ten-Eleven Translocation 2 to the human ICAM-1 promoter. Nucleic Acids Res 42(3):1563–1574. doi: 10.1093/nar/gkt1019
104. Maeder ML, Angstman JF, Richardson ME, Linder SJ, Cascio VM, Tsai SQ, Ho QH, Sander JD, Reyon D, Bernstein BE, Costello JF, Wilkinson MF, Joung JK (2013) Targeted DNA demethylation and activation of endogenous genes using programmable TALETET1 fusion proteins. Nat Biotechnol. doi: 10.1038/nbt.2726
105. Gifford CA, Ziller MJ, Gu H, Trapnell C, Donaghey J, Tsankov A, Shalek AK, Kelley DR, Shishkin AA, Issner R, Zhang X, Coyne M, Fostel JL, Holmes L, Meldrim J, Guttman M, Epstein C, Park H, Kohlbacher O, Rinn J, Gnirke A, Lander ES, Bernstein BE, Meissner A (2013) Transcriptional and epigenetic dynamics during specifi cation of human embryonic stem cells. Cell 153(5):1149–1163. doi: 10.1016/j.cell.2013.04.037
106. Sharma MD, Huang L, Choi JH, Lee EJ, Wilson JM, Lemos H, Pan F, Blazar BR, Pardoll DM, Mellor AL, Shi H, Munn DH (2013) An inherently bifunctional subset of Foxp3+ T helper cells is controlled by the transcription factor eos. Immunity 38(5):998–1012. doi: 10.1016/j.immuni.2013.01.013