Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409:860–921.
Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, et al. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature. 2007;447:167–77.
Koenig M, Monaco AP, Kunkel LM. The complete sequence of dystrophin predicts a rod-shaped cytoskeletal protein. Cell. 1988;53:219–28.
Bernstein BE, Meissner A, Lander ES. The mammalian epigenome. Cell. 2007;128:669–81.
Suzuki MM, Bird A. DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet. 2008;9:465–76.
Okano M, Bell DW, Haber DA, Li E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell. 1999;99:247–57.
Sharif J, Muto M, Takebayashi S-I, Suetake I, Iwamatsu A, Endo TA, et al. The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. Nature. 2007;450:908–12.
Ooi SKT, Bestor TH. The colorful history of active DNA demethylation. Cell. 2008;133:1145–8.
Ito S, Shen L, Dai Q, Wu SC, Collins LB, Swenberg JA, et al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science. 2011;333:1300–3.
Kohli RM, Zhang Y. TET enzymes, TDG and the dynamics of DNA demethylation. Nature. 2013;502:472–9.
He Y-F, Li B-Z, Li Z, Liu P, Wang Y, Tang Q, et al. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science. 2011;333:1303–7.
Maiti A, Drohat AC. Thymine DNA glycosylase can rapidly excise 5-formylcytosine and 5-carboxylcytosine: potential implications for active demethylation of CpG sites. J Biol Chem. 2011;286:35334–8.
Globisch D, Münzel M, Müller M, Michalakis S, Wagner M, Koch S, et al. Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS One. 2010;5:e15367.
Spruijt CG, Gnerlich F, Smits AH, Pfaffeneder T, Jansen PWTC, Bauer C, et al. Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell. 2013;152:1146–59.
Juan D, Perner J, Carrillo de Santa Pau E, Marsili S, Ochoa D, Chung H-R, et al. Epigenomic co-localization and co-evolution reveal a key role for 5hmC as a communication hub in the chromatin network of ESCs. Cell Rep. 2016;14:1246–57.
Suzuki M, Oda M, Ramos MP, Pascual M, Lau K, Stasiek E, et al. Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome. Genome Res. 2011;21:1833–40.
Baubec T, Colombo DF, Wirbelauer C, Schmidt J, Burger L, Krebs AR, et al. Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation. Nature. 2015;520:243–7.
Gilsbach R, Preissl S, Grüning BA, Schnick T, Burger L, Benes V, et al. Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease. Nat Commun. 2014;5:5288.
Jin L, Jiang Z, Xia Y, Lou P, Chen L, Wang H, et al. Genome-wide DNA methylation changes in skeletal muscle between young and middle-aged pigs. BMC Genomics. 2014;15:653.
Sim CB, Ziemann M, Kaspi A, Harikrishnan KN, Ooi J, Khurana I, et al. Dynamic changes in the cardiac methylome during postnatal development. FASEB J. 2015;29:1329–43.
Hahn MA, Qiu R, Wu X, Li AX, Zhang H, Wang J, et al. Dynamics of 5-hydroxymethylcytosine and chromatin marks in mammalian neurogenesis. Cell Rep. 2013;3:291–300.
Mellén M, Ayata P, Dewell S, Kriaucionis S, Heintz N. MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system. Cell. 2012;151:1417–30.
Wen L, Li X, Yan L, Tan Y, Li R, Zhao Y, et al. Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain. Genome Biol. 2014;15:R49.
Bird AP. CpG-rich islands and the function of DNA methylation. Nature. 1986;321:209–13.
Weber M, Hellmann I, Stadler MB, Ramos L, Pääbo S, Rebhan M, et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet. 2007;39:457–66.
Mouse Genome Sequencing Consortium, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002;420:520–62.
Irizarry RA. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 2003;31:15e–15.
Eisenberg E, Levanon EY. Human housekeeping genes, revisited. Trends Genet. 2013;29:569–74.
ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489:57–74.
Barski A, Cuddapah S, Cui K, Roh T-Y, Schones DE, Wang Z, et al. High-resolution profiling of histone methylations in the human genome. Cell. 2007;129:823–37.
Fong N, Saldi T, Sheridan RM, Cortazar MA, Bentley DL. RNA pol II dynamics modulate co-transcriptional chromatin modification, CTD phosphorylation, and transcriptional direction. Mol Cell. 2017;66:546–57. e3
Porrello ER, Mahmoud AI, Simpson E, Hill JA, Richardson JA, Olson EN, et al. Transient regenerative potential of the neonatal mouse heart. Science. 2011;331:1078–80.
Taub R. Liver regeneration: from myth to mechanism. Nat Rev Mol Cell Biol. 2004;5:836–47.
Ito S, D'Alessio AC, Taranova OV, Hong K, Sowers LC, Zhang Y. Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature. 2010;466:1129–33.
Diehl F, Brown MA, van Amerongen MJ, Novoyatleva T, Wietelmann A, Harriss J, et al. Cardiac deletion of Smyd2 is dispensable for mouse heart development. PLoS One. 2010;5:e9748.
Gottlieb PD, Pierce SA, Sims RJ, Yamagishi H, Weihe EK, Harriss JV, et al. Bop encodes a muscle-restricted protein containing MYND and SET domains and is essential for cardiac differentiation and morphogenesis. Nat Genet. 2002;31(31):25–32.
Wong NC, Wong LH, Quach JM, Canham P, Craig JM, Song JZ, et al. Permissive transcriptional activity at the centromere through pockets of DNA hypomethylation. PLoS Genet. 2006;2:e17.
Matus DQ, Lohmer LL, Kelley LC, Schindler AJ, Kohrman AQ, Barkoulas M, et al. Invasive cell fate requires G1 cell-cycle arrest and histone deacetylase-mediated changes in gene expression. Dev Cell. 2015;35:162–74.
Rinaldi L, Datta D, Serrat J, Morey L, Solanas G, Avgustinova A, et al. Dnmt3a and Dnmt3b associate with enhancers to regulate human epidermal stem cell homeostasis. Cell Stem Cell. 2016;19:491–501.
Song C-X, Szulwach KE, Dai Q, Fu Y, Mao S-Q, Lin L, et al. Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming. Cell. 2013;153:678–91.
Dubois-Chevalier J, Oger F, Dehondt H, Firmin FF, Gheeraert C, Staels B, et al. A dynamic CTCF chromatin binding landscape promotes DNA hydroxymethylation and transcriptional induction of adipocyte differentiation. Nucleic Acids Res. 2014;42:10943–59.
Wheldon LM, Abakir A, Ferjentsik Z, Dudnakova T, Strohbuecker S, Christie D, et al. Transient accumulation of 5-carboxylcytosine indicates involvement of active demethylation in lineage specification of neural stem cells. Cell Rep. 2014;7:1353–61.
Kanno T, Kanno Y, LeRoy G, Campos E, Sun H-W, Brooks SR, et al. BRD4 assists elongation of both coding and enhancer RNAs by interacting with acetylated histones. Nat Struct Mol Biol. 2014;21:1047–57.
Anand P, Brown JD, Lin CY, Qi J, Zhang R, Artero PC, et al. BET bromodomains mediate transcriptional pause release in heart failure. Cell. 2013;154:569–82.
Subramanian S, Kumar S. Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome. Genetics Genetics. 2004;168:373–81.
Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, et al. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science. 2002;298:2157–67.
Münzel M, Globisch D, Brückl T, Wagner M, Welzmiller V, Michalakis S, et al. Quantification of the sixth DNA base hydroxymethylcytosine in the brain. Angew Chem Int Ed Engl. 2010;49:5375–7.
Hattori F, Chen H, Yamashita H, Tohyama S, Satoh Y-S, Yuasa S, et al. Nongenetic method for purifying stem cell–derived cardiomyocytes. Nat Methods. 2009;7:61–6.
Ieda M, Tsuchihashi T, Ivey KN, Ross RS, Hong T-T, Shaw RM, et al. Cardiac fibroblasts regulate myocardial proliferation through beta1 integrin signaling. Dev Cell. 2009;16:233–44.
Suzuki M, Jing Q, Lia D, Pascual M, McLellan A, Greally JM. Optimized design and data analysis of tag-based cytosine methylation assays. Genome Biol. 2010;11:R36.
Jing Q, McLellan A, Greally JM, Suzuki M. Automated computational analysis of genome-wide DNA methylation profiling data from HELP-tagging assays. Methods Mol Biol. 2012;815:79–87.
Song C-X, Szulwach KE, Fu Y, Dai Q, Yi C, Li X, et al. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotechnol. 2011;29:68–72.
Wei C, Qiu J, Zhou Y, Xue Y, Hu J, Ouyang K, et al. Repression of the central splicing regulator RBFox2 is functionally linked to pressure overload-induced heart failure. Cell Rep. 2015;10:1521–33.
Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9:357–9.
Shen L, Shao N, Liu X, Nestler E. Ngs.Plot: quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics. 2014;15:284.