1. OkitaK, IchisakaT, YamanakaS (2007) Generation of germline-competent induced pluripotent stem cells. Nature 448: 313–317.
2. SilvaJ, BarrandonO, NicholsJ, KawaguchiJ, TheunissenTW, et al. (2008) Promotion of reprogramming to ground state pluripotency by signal inhibition. PLoS Biol 6: e253.
3. HeintzmanND, HonGC, HawkinsRD, KheradpourP, StarkA, et al. (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459: 108–112.
4. Rada-IglesiasA, BajpaiR, SwigutT, BrugmannSA, FlynnRA, et al. (2011) A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470: 279–283.
5. LupienM, EeckhouteJ, MeyerCA, WangQ, ZhangY, et al. (2008) FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell 132: 958–970.
6. HodgesE, MolaroA, Dos SantosCO, ThekkatP, SongQ, et al. (2011) Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol Cell 44: 17–28.
7. StadlerMB, MurrR, BurgerL, IvanekR, LienertF, et al. (2011) DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480: 490–495.
8. WienchM, JohnS, BaekS, JohnsonTA, SungMH, et al. (2011) DNA methylation status predicts cell type-specific enhancer activity. EMBO J 30: 3028–3039.
9. BurgerL, GaidatzisD, SchubelerD, StadlerMB (2013) Identification of active regulatory regions from DNA methylation data. Nucleic Acids Res
10. HonGC, RajagopalN, ShenY, McClearyDF, YueF, et al. (2013) Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nat Genet
11. ZillerMJ, GuH, MullerF, DonagheyJ, TsaiLT, et al. (2013) Charting a dynamic DNA methylation landscape of the human genome. Nature 500: 477–481.
12. BhutaniN, BurnsDM, BlauHM (2011) DNA demethylation dynamics. Cell 146: 866–872.
13. HeYF, LiBZ, LiZ, LiuP, WangY, et al. (2011) Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 333: 1303–1307.
14. InoueA, ZhangY (2011) Replication-dependent loss of 5-hydroxymethylcytosine in mouse preimplantation embryos. Science 334: 194.
15. KriaucionisS, HeintzN (2009) The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324: 929–930.
16. TahilianiM, KohKP, ShenY, PastorWA, BandukwalaH, et al. (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324: 930–935.
17. PastorWA, PapeUJ, HuangY, HendersonHR, ListerR, et al. (2011) Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature 473: 394–397.
18. SerandourAA, AvnerS, OgerF, BizotM, PercevaultF, et al. Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers. Nucleic Acids Res 40: 8255–8265.
19. StroudH, FengS, Morey KinneyS, PradhanS, JacobsenSE (2011) 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells. Genome Biol 12: R54.
20. SzulwachKE, LiX, LiY, SongCX, HanJW, et al. (2011) Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. PLoS Genet 7: e1002154.
21. YuM, HonGC, SzulwachKE, SongCX, ZhangL, et al. (2012) Base-resolution analysis of 5-hydroxymethylcytosine in the Mammalian genome. Cell 149: 1368–1380.
22. GlobischD, MunzelM, MullerM, MichalakisS, WagnerM, et al. (2010) Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS One 5: e15367.
23. NestorCE, OttavianoR, ReddingtonJ, SproulD, ReinhardtD, et al. Tissue type is a major modifier of the 5-hydroxymethylcytosine content of human genes. Genome Res 22: 467–477.
24. BellAC, FelsenfeldG (2000) Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature 405: 482–485.
25. XieW, BarrCL, KimA, YueF, LeeAY, et al. (2012) Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome. Cell 148: 816–831.
26. BrinkmanAB, GuH, BartelsSJ, ZhangY, MatareseF, et al. (2012) Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res 22: 1128–1138.
27. StathamAL, RobinsonMD, SongJZ, CoolenMW, StirzakerC, et al. (2012) Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA. Genome Res 22: 1120–1127.
28. RheeHS, PughBF Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell 147: 1408–1419.
29. HuangY, PastorWA, ShenY, TahilianiM, LiuDR, et al. (2010) The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing. PLoS One 5: e8888.
30. JinSG, KadamS, PfeiferGP (2010) Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine. Nucleic Acids Res 38: e125.
31. FiczG, BrancoMR, SeisenbergerS, SantosF, KruegerF, et al. (2011) Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature 473: 398–402.
32. WilliamsK, ChristensenJ, PedersenMT, JohansenJV, CloosPA, et al. (2011) TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 473: 343–348.
33. WuH, D'AlessioAC, ItoS, XiaK, WangZ, et al. (2011) Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells. Nature 473: 389–393.
34. BibelM, RichterJ, LacroixE, BardeYA (2007) Generation of a defined and uniform population of CNS progenitors and neurons from mouse embryonic stem cells. Nat Protoc 2: 1034–1043.
35. FedoriwAM, SteinP, SvobodaP, SchultzRM, BartolomeiMS (2004) Transgenic RNAi reveals essential function for CTCF in H19 gene imprinting. Science 303: 238–240.
36. HeathH, Ribeiro de AlmeidaC, SleutelsF, DingjanG, van de NobelenS, et al. (2008) CTCF regulates cell cycle progression of alphabeta T cells in the thymus. EMBO J 27: 2839–2850.
37. HirayamaT, TarusawaE, YoshimuraY, GaljartN, YagiT (2012) CTCF is required for neural development and stochastic expression of clustered Pcdh genes in neurons. Cell Rep 2: 345–357.
38. SoshnikovaN, MontavonT, LeleuM, GaljartN, DubouleD (2010) Functional analysis of CTCF during mammalian limb development. Dev Cell 19: 819–830.
39. SchmidtD, SchwaliePC, WilsonMD, BallesterB, GoncalvesA, et al. (2012) Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell 148: 335–348.
40. TanL, XiongL, XuW, WuF, HuangN, et al. Genome-wide comparison of DNA hydroxymethylation in mouse embryonic stem cells and neural progenitor cells by a new comparative hMeDIP-seq method. Nucleic Acids Res
41. DingJ, XuH, FaiolaF, Ma'ayanA, WangJ (2012) Oct4 links multiple epigenetic pathways to the pluripotency network. Cell Res 22: 155–167.
42. SerandourAA, AvnerS, PercevaultF, DemayF, BizotM, et al. (2011) Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers. Genome Res 21: 555–565.
43. FuY, SinhaM, PetersonCL, WengZ (2008) The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet 4: e1000138.
44. FrauerC, HoffmannT, BultmannS, CasaV, CardosoMC, et al. Recognition of 5-hydroxymethylcytosine by the Uhrf1 SRA domain. PLoS One 6: e21306.
45. KubosakiA, TomaruY, FuruhataE, SuzukiT, ShinJW, et al. CpG site-specific alteration of hydroxymethylcytosine to methylcytosine beyond DNA replication. Biochem Biophys Res Commun 426: 141–147.
46. ShenL, WuH, DiepD, YamaguchiS, D'AlessioAC, et al. (2013) Genome-wide Analysis Reveals TET- and TDG-Dependent 5-methylcytosine Oxidation Dynamics. Cell 153.
47. SongCX, SzulwachKE, DaiQ, FuY, MaoSQ, et al. (2013) Genome-wide profiling of 5-Formylcytosine reveals its roles in epigenetic priming. Cell
48. ValinluckV, SowersLC (2007) Endogenous cytosine damage products alter the site selectivity of human DNA maintenance methyltransferase DNMT1. Cancer Res 67: 946–950.
49. MellenM, AyataP, DewellS, KriaucionisS, HeintzN MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system. Cell 151: 1417–1430.
50. YildirimO, LiR, HungJH, ChenPB, DongX, et al. Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells. Cell 147: 1498–1510.
51. BaubecT, IvanekR, LienertF, SchubelerD Methylation-Dependent and -Independent Genomic Targeting Principles of the MBD Protein Family. Cell 153: 480–492.
52. SpruijtCG, GnerlichF, SmitsAH, PfaffenederT, JansenPW, et al. Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell 152: 1146–1159.
53. JonesPA (2012) Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 13: 484–492.
54. SchubelerD Molecular biology. Epigenetic islands in a genetic ocean. Science 338: 756–757.
55. DeatonAM, BirdA (2011) CpG islands and the regulation of transcription. Genes Dev 25: 1010–1022.
56. MohnF, WeberM, SchubelerD, RoloffTC (2009) Methylated DNA immunoprecipitation (MeDIP). Methods Mol Biol 507: 55–64.
57. LangmeadB, TrapnellC, PopM, SalzbergSL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
58. ArnoldP, ScholerA, PachkovM, BalwierzPJ, JorgensenH, et al. Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting. Genome Res 23: 60–73.