High-resolution genome-wide DNA methylation maps of mouse primary female dermal fibroblasts and keratinocytes

Epigenetics and Chromatin

Volumn 7, Issue 1, 2014, Pages

  Chatterjee, Raghunath ^a,b   He, Ximiao ^a   Huang, Di ^c   Fitzgerald, Peter ^a   Smith, Andrew ^d   Vinson, Charles ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b INDIAN STATISTICAL INSTITUTE   (India)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

^d UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

C EBP ; CG methylation; CTCF; Fibroblasts; HMR; Hypomethylated regions; Keratinocytes; Methylome

Indexed keywords

CCAAT ENHANCER BINDING PROTEIN BETA; CYTOSINE; DINUCLEOTIDE; DNA; MESSENGER RNA; TRANSCRIPTION FACTOR CTCF;

ANIMAL CELL; ARTICLE; BINDING SITE; DEMETHYLATION; DNA METHYLATION; EXON; FEMALE; GENE EXPRESSION; GENE MAPPING; GENE REPRESSION; KERATINOCYTE; MOUSE; NEWBORN; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; RNA SEQUENCE; SKIN FIBROBLAST;

MAMMALIA;

EID: 84924100372     PISSN: None     EISSN: 17568935     Source Type: Journal    
DOI: 10.1186/1756-8935-7-35     Document Type: Article

References (61)

1. Bird AP, Taggart MH, Smith BA: Methylated and unmethylated DNA compartments in the sea urchin genome. Cell 1979, 17:889-901.
2. Noyer-Weidner M, Trautner TA: Methylation of DNA in prokaryotes. EXS 1993, 64:39-108.
3. Jeltsch A: Molecular biology: phylogeny of methylomes. Science 2010, 328:837-838.
4. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR: Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 2008, 133:523-536.
5. 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: Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009, 462:315-322.
6. Bird AP: DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res 1980, 8:1499-1504.
7. Gardiner-Garden M, Frommer M: CpG islands in vertebrate genomes. J Mol Biol 1987, 196:261-282.
8. Rishi V, Bhattacharya P, Chatterjee R, Rozenberg J, Zhao J, Glass K, Fitzgerald P, Vinson C: CpG methylation of half-CRE sequences creates C/EBPalpha binding sites that activate some tissue-specific genes. Proc Natl Acad Sci U S A 2010, 107:20311-20316.
9. Rougier N, Bourc'his D, Gomes DM, Niveleau A, Plachot M, Paldi A, Viegas-Pequignot E: Chromosome methylation patterns during mammalian preimplantation development. Genes Dev 1998, 12:2108-2113.
10. Reik W, Dean W, Walter J: Epigenetic reprogramming in mammalian development. Science 2001, 293:1089-1093.
11. Reik W, Walter J: Genomic imprinting: parental influence on the genome. Nat Rev Genet 2001, 2:21-32.
12. Takizawa T, Nakashima K, Namihira M, Ochiai W, Uemura A, Yanagisawa M, Fujita N, Nakao M, Taga T: DNA methylation is a critical cell-intrinsic determinant of astrocyte differentiation in the fetal brain. Dev Cell 2001, 1:749-758.
13. Bird A: DNA methylation patterns and epigenetic memory. Genes Dev 2002, 16:6-21.
14. Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB, Gnirke A, Jaenisch R, Lander ES: Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 2008, 454:766-770.
15. Laurent L, Wong E, Li G, Huynh T, Tsirigos A, Ong CT, Low HM, Kin Sung KW, Rigoutsos I, Loring J, Wei CL: Dynamic changes in the human methylome during differentiation. Genome Res 2010, 20:320-331.
16. Baylin SB, Jones PA: A decade of exploring the cancer epigenome - biological and translational implications. Nat Rev Cancer 2011, 11:726-734.
17. Rodriguez-Paredes M, Esteller M: Cancer epigenetics reaches mainstream oncology. Nat Med 2011, 17:330-339.
18. Molaro A, Hodges E, Fang F, Song Q, McCombie WR, Hannon GJ, Smith AD: Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates. Cell 2011, 146:1029-1041.
19. Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Scholer A, Van Nimwegen E, Wirbelauer C, Oakeley EJ, Gaidatzis D, Tiwari VK, Schübeler D: DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 2011, 480:490-495.
20. Varley KE, Gertz J, Bowling KM, Parker SL, Reddy TE, Pauli-Behn F, Cross MK, Williams BA, Stamatoyannopoulos JA, Crawford GE, Absher DM, Wold BJ, Myers RM: Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res 2013, 23:555-567.
21. Lyko F, Foret S, Kucharski R, Wolf S, Falckenhayn C, Maleszka R: The honey bee epigenomes: differential methylation of brain DNA in queens and workers. PLoS Biol 2010, 8:e1000506.
22. Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M, Ji H, Potash JB, Sabunciyan S, Feinberg AP: The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 2009, 41:178-186.
23. Ball MP, Li JB, Gao Y, Lee JH, Le Proust EM, Park IH, Xie B, Daley GQ, Church GM: Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol 2009, 27:361-368.
24. Zemach A, McDaniel IE, Silva P, Zilberman D: Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 2010, 328:916-919.
25. Rakyan VK, Down TA, Thorne NP, Flicek P, Kulesha E, Graf S, Tomazou EM, Backdahl L, Johnson N, Herberth M, Howe KL, Jackson DK, Miretti MM, Fiegler H, Marioni JC, Birney E, Hubbard TJ, Carter NP, Tavare S, Beck S: An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res 2008, 18:1518-1529.
26. Yagi S, Hirabayashi K, Sato S, Li W, Takahashi Y, Hirakawa T, Wu G, Hattori N, Ohgane J, Tanaka S, Liu XS, Shiota K: DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression. Genome Res 2008, 18:1969-1978.
27. Krivega I, Dean A: Enhancer and promoter interactions-long distance calls. Curr Opin Genet Dev 2011, 22:79-85.
28. Ziller MJ, Gu H, Muller F, Donaghey J, Tsai LT, Kohlbacher O, De Jager PL, Rosen ED, Bennett DA, Bernstein BE, Gnirke A, Meissner A: Charting a dynamic DNA methylation landscape of the human genome. Nature 2013, 500:477-481.
29. Hodges E, Molaro A, Dos Santos CO, Thekkat P, Song Q, Uren PJ, Park J, Butler J, Rafii S, McCombie WR, Smith AD, Hannon GJ: Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol Cell 2011, 44:17-28.
30. McDonald OG, Wu H, Timp W, Doi A, Feinberg AP: Genome-scale epigenetic reprogramming during epithelial-to-mesenchymal transition. Nat Struct Mol Biol 2011, 18:867-874.
31. Mann IK, Chatterjee R, Zhao J, He X, Weirauch MT, Hughes TR, Vinson C: CG methylated microarrays identify a novel methylated sequence bound by the CEBPB|ATF4 heterodimer that are active in vivo. Genome Res 2013, 23:988-997.
32. Chodavarapu RK, Feng S, Bernatavichute YV, Chen PY, Stroud H, Yu Y, Hetzel JA, Kuo F, Kim J, Cokus SJ, Casero D, Bernal M, Huijser P, Clark AT, Kramer U, Merchant SS, Zhang X, Jacobsen SE, Pellegrini M: Relationship between nucleosome positioning and DNA methylation. Nature 2010, 466:388-392.
33. Hogart A, Lichtenberg J, Ajay SS, Anderson S, Margulies EH, Bodine DM: Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites. Genome Res 2012, 22:1407-1418.
34. Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A: Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res 2010, 20:110-121.
35. Ponger L, Mouchiroud D: CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences. Bioinformatics 2002, 18:631-633.
36. Illingworth RS, Gruenewald-Schneider U, Webb S, Kerr AR, James KD, Turner DJ, Smith C, Harrison DJ, Andrews R, Bird AP: Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet 2010, 6:e1001134.
37. Estecio MR, Gallegos J, Vallot C, Castoro RJ, Chung W, Maegawa S, Oki Y, Kondo Y, Jelinek J, Shen L, Hartung H, Aplan PD, Czerniak BA, Liang S, Issa JP: Genome architecture marked by retrotransposons modulates predisposition to DNA methylation in cancer. Genome Res 2010, 20:1369-1382.
38. Estecio MR, Gallegos J, Dekmezian M, Lu Y, Liang S, Issa JP: SINE retrotransposons cause epigenetic reprogramming of adjacent gene promoters. Mol Cancer Res 2012, 10:1332-1342.
39. Morasso MI, Radoja N: Dlx genes, p63, and ectodermal dysplasias. Birth Defects Res C Embryo Today 2005, 75:163-171.
40. Cortes C, Vapnik V: Support-vector networks. Mach Learn 1995, 20:273-297.
41. Busser BW, Taher L, Kim Y, Tansey T, Bloom MJ, Ovcharenko I, Michelson AM: A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis. PLoS Genet 2012, 8:e1002531.
42. Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, Voss N, Stegmaier P, Lewicki-Potapov B, Saxel H, Kel AE, Wingender E: TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res 2006, 34:D108-D110.
43. Grontved L, John S, Baek S, Liu Y, Buckley JR, Vinson C, Aguilera G, Hager GL: C/EBP maintains chromatin accessibility in liver and facilitates glucocorticoid receptor recruitment to steroid response elements. EMBO J 2013, 32:1568-1583.
44. Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, Epstein CB, Frietze S, Harrow J, Kaul R, Khatun J, Lajoie BR, Landt SG, Lee BK, Pauli F, Rosenbloom KR, Sabo P, Safi A, Sanyal A, Shoresh N, Simon JM, Song L, Trinklein ND, Altshuler RC, Birney E, Brown JB, Cheng C, Djebali S, Dong X, Ernst J, et al: An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489:57-74.
45. Bell AC, West AG, Felsenfeld G: The protein CTCF is required for the enhancer blocking activity of vertebrate insulators. Cell 1999, 98:387-396.
46. Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, Zhang MQ, Lobanenkov VV, Ren B: Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 2007, 128:1231-1245.
47. Cuddapah S, Jothi R, Schones DE, Roh TY, Cui K, Zhao K: Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Res 2009, 19:24-32
48. Wang H, Maurano MT, Qu H, Varley KE, Gertz J, Pauli F, Lee K, Canfield T, Weaver M, Sandstrom R, Thurman RE, Kaul R, Myers RM, Stamatoyannopoulos JA: Widespread plasticity in CTCF occupancy linked to DNA methylation. Genome Res 2012, 22:1680-1688
49. Shukla S, Kavak E, Gregory M, Imashimizu M, Shutinoski B, Kashlev M, Oberdoerffer P, Sandberg R, Oberdoerffer S: CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature 2011, 479:74-79
50. Bao L, Zhou M, Cui Y: CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators. Nucleic Acids Res 2008, 36D83-D87
51. Bird AP: CpG-rich islands and the function of DNA methylation. Nature 1986, 321:209-213.
52. Zemach A, Zilberman D: Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Curr Biol 2010, 20:R780-R785
53. Hermann R, Doerfler W: Interference with protein binding at AP2 sites by sequence-specific methylation in the late E2A promoter of adenovirus type 2 DNA. FEBS Lett 1991, 281:191-195
54. McDade SS, Henry AE, Pivato GP, Kozarewa I, Mitsopoulos C, Fenwick K, Assiotis I, Hakas J, Zvelebil M, Orr N, Lord CJ, Patel D, Ashworth A, McCance DJ: Genome-wide analysis of p63 binding sites identifies AP-2 factors as co-regulators of epidermal differentiation. Nucleic Acids Res 2012, 40:7190-7206.
55. Rozenberg JM, Shlyakhtenko A, Glass K, Rishi V, Myakishev MV, Fitz Gerald PC, Vinson C: All and only CpG containing sequences are enriched in promoters abundantly bound by RNA polymerase II in multiple tissues. BMC Genomics 2008, 9:67.
56. Campanero MR, Armstrong MI, Flemington EK: CpG methylation as a mechanism for the regulation of E2F activity. Proc Natl Acad Sci USA 2000, 97:6481-6486.
57. Reamon-Buettner SM, Borlak J: Epigenetic silencing of cell adhesion molecule 1 in different cancer progenitor cells of transgenic c-Myc and c-Raf mouse lung tumors. Cancer Res 2008, 68:7587-7596
58. Pastor WA, Aravind L, Rao A: TETonic shift: biological roles of TET proteins in DNA demethylation and transcription. Nat Rev Mol Cell Biol 2013, 14:341-356.
59. Sanchez Alvarado A, Yamanaka S: Rethinking differentiation: stem cells, regeneration, and plasticity. Cell 2014, 157:110-119
60. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS: Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008, 9:R137.
61. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS: MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 2009, 37:W202-W208.