Ramsahoye, B.H. et al. Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc. Natl. Acad. Sci. USA 97, 5237–5242 (2000).
Lister, R. et al. Global epigenomic reconfiguration during mammalian brain development. Science 341, 1237905 (2013).
Jurkowska, R.Z., Jurkowski, T.P. & Jeltsch, A. Structure and function of mammalian DNA methyltransferases. ChemBioChem 12, 206–222 (2011).
Arand, J. et al. In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases. PLoS Genet. 8, e1002750 (2012).
Liang, G. et al. Cooperativity between DNA methyltransferases in the maintenance methylation of repetitive elements. Mol. Cell. Biol. 22, 480–491 (2002).
Iguchi-Ariga, S.M. & Schaffner, W. CpG methylation of the cAMP-responsive enhancer/promoter sequence TGACGTCA abolishes specific factor binding as well as transcriptional activation. Genes Dev. 3, 612–619 (1989).
Campanero, M.R., Armstrong, M.I. & Flemington, E.K. CpG methylation as a mechanism for the regulation of E2F activity. Proc. Natl. Acad. Sci. USA 97, 6481–6486 (2000).
Prendergast, G.C. & Ziff, E.B. Methylation-sensitive sequence-specific DNA binding by the c-Myc basic region. Science 251, 186–189 (1991).
Blattler, A. & Farnham, P.J. Cross-talk between site-specific transcription factors and DNA methylation states. J. Biol. Chem. 288, 34287–34294 (2013).
Bakker, J., Lin, X. & Nelson, W.G. Methyl-CpG binding domain protein 2 represses transcription from hypermethylated -class glutathione S-transferase gene promoters in hepatocellular carcinoma cells. J. Biol. Chem. 277, 22573–22580 (2002).
Jiang, C.L. et al. MBD3L1 and MBD3L2, two new proteins homologous to the methyl-CpG-binding proteins MBD2 and MBD3: characterization of MBD3L1 as a testis-specific transcriptional repressor. Genomics 80, 621–629 (2002).
Baubec, T. et al. Methylation-dependent and -independent genomic targeting principles of the MBD protein family. Cell 153, 480–492 (2013). In this paper, a correlation between genome-wide MBD binding and mCpG density is shown.
Curradi, M. et al. Molecular mechanisms of gene silencing mediated by DNA methylation. Mol. Cell. Biol. 22, 3157–3173 (2002).
Huff, J.T. & Zilberman, D. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell 156, 1286–1297 (2014).
Thomson, J.P. et al. CpG islands influence chromatin structure via the CpG-binding protein Cfp1. Nature 464, 1082–1086 (2010). This is the first paper showing that nonmethylated CpG-rich sequences recruit CXXC domain–containing activator proteins.
Farcas, A.M. et al. KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands. Elife 1, e00205 (2012).
Blackledge, N.P. et al. Variant PRC1 complex-dependent H2A ubiquitylation drives PRC2 recruitment and Polycomb domain formation. Cell 157, 1445–1459 (2014).
Kass, S.U., Landsberger, N. & Wolffe, A.P. DNA methylation directs a time-dependent repression of transcription initiation. Curr. Biol. 7, 157–165 (1997).
Jones, P.L. et al. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat. Genet. 19, 187–191 (1998).
Defossez, P.A. & Stancheva, I. Biological functions of methyl-CpG-binding proteins. Prog. Mol. Biol. Transl. Sci. 101, 377–398 (2011).
Bogdanovicć, O. & Veenstra, G.J. DNA methylation and methyl-CpG binding proteins: developmental requirements and function. Chromosoma 118, 549–565 (2009).
Filion, G.J. et al. A family of human zinc finger proteins that bind methylated DNA and repress transcription. Mol. Cell. Biol. 26, 169–181 (2006).
Laget, S. et al. The human proteins MBD5 and MBD6 associate with heterochromatin but they do not bind methylated DNA. PLoS ONE 5, e11982 (2010).
Laherty, C.D. et al. Histone deacetylases associated with the mSin3 corepressor mediate Mad transcriptional repression. Cell 89, 349–356 (1997).
Nagy, L. et al. Nuclear receptor repression mediated by a complex containing SMRT, mSin3A, and histone deacetylase. Cell 89, 373–380 (1997).
Lyst, M.J. et al. Rett syndrome mutations abolish the interaction of MeCP2 with the NCoR/SMRT co-repressor. Nat. Neurosci. 16, 898–902 (2013).
Le Guezennec, X. et al. MBD2/NuRD and MBD3/NuRD, two distinct complexes with different biochemical and functional properties. Mol. Cell. Biol. 26, 843–851 (2006).
Ng, H.H. et al. MBD2 is a transcriptional repressor belonging to the MeCP1 histone deacetylase complex. Nat. Genet. 23, 58–61 (1999).
Dong, S.M. et al. Promoter hypermethylation of multiple genes in carcinoma of the uterine cervix. Clin. Cancer Res. 7, 1982–1986 (2001).
Kang, S.H. et al. Transcriptional repression of the transforming growth factor- type I receptor gene by DNA methylation results in the development of TGF- resistance in human gastric cancer. Oncogene 18, 7280–7286 (1999).
Chiurazzi, P. et al. In vitro reactivation of the FMR1 gene involved in fragile X syndrome. Hum. Mol. Genet. 7, 109–113 (1998).
Robert, M.F. et al. DNMT1 is required to maintain CpG methylation and aberrant gene silencing in human cancer cells. Nat. Genet. 33, 61–65 (2003).
Bartels, S.J. et al. A SILAC-based screen for methyl-CpG binding proteins identifies RBP-J as a DNA methylation and sequence-specific binding protein. PLoS ONE 6, e25884 (2011).
Bartke, T. et al. Nucleosome-interacting proteins regulated by DNA and histone methylation. Cell 143, 470–484 (2010).
Mittler, G., Butter, F. & Mann, M. A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements. Genome Res. 19, 284–293 (2009).
Spruijt, C.G. et al. Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell 152, 1146–1159 (2013). In this paper, a comprehensive catalog of readers for mC and hmC in different cell types is presented.
Hu, S. et al. DNA methylation presents distinct binding sites for human transcription factors. Elife 2, e00726 (2013). This paper reveals that a large number of transcription factors interact with DNA sequences containing methylated CpGs.
Liu, Y. et al. Structural basis for Klf4 recognition of methylated DNA. Nucleic Acids Res. 42, 4859–4867 (2014).
Lewitzky, M. & Yamanaka, S. Reprogramming somatic cells towards pluripotency by defined factors. Curr. Opin. Biotechnol. 18, 467–473 (2007).
Liu, Y. et al. An atomic model of Zfp57 recognition of CpG methylation within a specific DNA sequence. Genes Dev. 26, 2374–2379 (2012).
Rishi, V. et al. CpG methylation of half-CRE sequences creates C/EBPα binding sites that activate some tissue-specific genes. Proc. Natl. Acad. Sci. USA 107, 20311–20316 (2010). This paper shows that the transcription factor C/EBPα binds to a methylated CRE sequence to activate transcription during differentiation.
Sasai, N., Nakao, M. & Defossez, P.A. Sequence-specific recognition of methylated DNA by human zinc-finger proteins. Nucleic Acids Res. 38, 5015–5022 (2010).
Mackay, D.J. et al. Hypomethylation of multiple imprinted loci in individuals with transient neonatal diabetes is associated with mutations in ZFP57. Nat. Genet. 40, 949–951 (2008).
Quenneville, S. et al. In embryonic stem cells, ZFP57/KAP1 recognize a methylated hexanucleotide to affect chromatin and DNA methylation of imprinting control regions. Mol. Cell 44, 361–372 (2011).
Brinkman, A.B. et al. Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res. 22, 1128–1138 (2012).
Tahiliani, M. et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930–935 (2009).
Kriaucionis, S. & Heintz, N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324, 929–930 (2009).
Münzel, M. et al. Quantification of the sixth DNA base hydroxymethylcytosine in the brain. Angew. Chem. Int. Edn Engl. 49, 5375–5377 (2010).
Ito, S. et al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333, 1300–1303 (2011).
Maiti, A. et al. TDG excision of fC may be a predominant element of pathways for active DNA demethylation. FASEB J. 27, 758.6 (2013).
Wu, H. & Zhang, Y. Reversing DNA methylation: mechanisms, genomics, and biological functions. Cell 156, 45–68 (2014).
Iurlaro, M. et al. A screen for hydroxymethylcytosine and formylcytosine binding proteins suggests functions in transcription and chromatin regulation. Genome Biol. 14, R119 (2013).
Mellén, M. et al. MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system. Cell 151, 1417–1430 (2012).
Hashimoto, H. et al. Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation. Nucleic Acids Res. 40, 4841–4849 (2012).
Valinluck, V. et al. Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2). Nucleic Acids Res. 32, 4100–4108 (2004).
Khrapunov, S. et al. Unusual characteristics of the DNA binding domain of epigenetic regulatory protein MeCP2 determine its binding specificity. Biochemistry 53, 3379–3391 (2014).
Yildirim, O. et al. Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells. Cell 147, 1498–1510 (2011).
Frauer, C. et al. Recognition of 5-hydroxymethylcytosine by the Uhrf1 SRA domain. PLoS ONE 6, e21306 (2011).
Zhou, T. et al. Structural basis for hydroxymethylcytosine recognition by the SRA domain of UHRF2. Mol. Cell 54, 879–886 (2014).
Booth, M.J. et al. Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science 336, 934–937 (2012).
Li, Y., Song, C.X., He, C. & Jin, P. Selective capture of 5-hydroxymethylcytosine from genomic DNA. J. Vis. Exp. 68, e4441 (2012).
Song, C.X. et al. Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming. Cell 153, 678–691 (2013).
Ogoshi, K. et al. Genome-wide profiling of DNA methylation in human cancer cells. Genomics 98, 280–287 (2011).
Aran, D. et al. Replication timing-related and gene body-specific methylation of active human genes. Hum. Mol. Genet. 20, 670–680 (2011).
Hellman, A. & Chess, A. Gene body-specific methylation on the active X chromosome. Science 315, 1141–1143 (2007).
Jjingo, D. et al. On the presence and role of human gene-body DNA methylation. Oncotarget 3, 462–474 (2012).
Maunakea, A.K. et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 466, 253–257 (2010).
Hogart, A. et al. Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites. Genome Res. 22, 1407–1418 (2012).
Hon, G.C. et al. Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nat. Genet. 45, 1198–1206 (2013).
Ziller, M.J. et al. Charting a dynamic DNA methylation landscape of the human genome. Nature 500, 477–481 (2013).
Xie, W. et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell 153, 1134–1148 (2013).
Kulis, M. et al. Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia. Nat. Genet. 44, 1236–1242 (2012).
Seisenberger, S. et al. The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells. Mol. Cell 48, 849–862 (2012).
Hammoud, S.S. et al. Chromatin and transcription transitions of mammalian adult germline stem cells and spermatogenesis. Cell Stem Cell 15, 239–253 (2014). This paper shows that many methylated CpG-island promoters in male germ cells are actively transcribed.
Bogdanovic, O. et al. Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis. Genome Res. 21, 1313–1327 (2011). This paper reveals a temporal uncoupling between CpG-island methylation and repression of transcription during early Xenopus laevis development.
Fouse, S.D. et al. Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation. Cell Stem Cell 2, 160–169 (2008).
Baubec, T. & Schubeler, D. Genomic patterns and context specific interpretation of DNA methylation. Curr. Opin. Genet. Dev. 25, 85–92 (2014).
Jones, P.A. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat. Rev. Genet. 13, 484–492 (2012).
Boyes, J. & Bird, A. Repression of genes by DNA methylation depends on CpG density and promoter strength: evidence for involvement of a methyl-CpG binding protein. EMBO J. 11, 327–333 (1992).
Hsieh, C.L. Dependence of transcriptional repression on CpG methylation density. Mol. Cell. Biol. 14, 5487–5494 (1994).
Lu, Y. et al. Alternative splicing of MBD2 supports self-renewal in human pluripotent stem cells. Cell Stem Cell 15, 192–101 (2014).
Tao, J. et al. Phosphorylation of MeCP2 at Serine 80 regulates its chromatin association and neurological function. Proc. Natl. Acad. Sci. USA 106, 4882–4887 (2009).
Donaldson, N.S. et al. Kaiso regulates Znf131-mediated transcriptional activation. Exp. Cell Res. 316, 1692–1705 (2010).
Solomon, D.L., Amati, B. & Land, H. Distinct DNA binding preferences for the c-Myc/Max and Max/Max dimers. Nucleic Acids Res. 21, 5372–5376 (1993).