Mohn F, Schübeler D. Genetics and epigenetics: stability and plasticity during cellular differentiation. Trends in Genetics. 2009;25(3):129–36. doi:10.1016/j.tig.2008.12.005.
Article
CAS
PubMed
Google Scholar
Berdasco M, Esteller M. DNA methylation in stem cell renewal and multipotency. Stem Cell Res Ther. 2011;2(5):42. doi:10.1186/scrt83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cedar H, Bergman Y. Programming of DNA methylation patterns. Annu Rev Biochem. 2012;2012(81):97–117. doi:10.1146/annurev-biochem-052610-91920.
Article
Google Scholar
Smith ZD, Meissner A. DNA methylation: roles in mammalian development. Nat Rev Genet. 2013;14(3):204–20. doi:10.1038/nrg3354.
Article
CAS
PubMed
Google Scholar
Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012;13(7):484–92. doi:10.1038/nrg3230.
Article
CAS
PubMed
Google Scholar
Rakyan VK, Down TA, Thorne NP, Flicek P, Kulesha E, Graf S, et al. An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res. 2008;18(9):1518–29. doi:10.1101/gr.077479.108.
Article
CAS
PubMed
PubMed Central
Google Scholar
Straussman R, Nejman D, Roberts D, Steinfeld I, Blum B, Benvenisty N, et al. Developmental programming of CpG island methylation profiles in the human genome. Nat Struct Mol Biol. 2009;16(5):564–71. doi:10.1038/nsmb.1594.
Article
CAS
PubMed
Google Scholar
Fernandez AF, Assenov Y, Martin-Subero JI, Balint B, Siebert R, Taniguchi H, et al. A DNA methylation fingerprint of 1628 human samples. Genome Res. 2012;22(2):407–19. doi:10.1101/gr.119867.110.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nagae G, Isagawa T, Shiraki N, Fujita T, Yamamoto S, Tsutsumi S, et al. Tissue-specific demethylation in CpG-poor promoters during cellular differentiation. Hum Mol Genet. 2011;20(14):2710–21. doi:10.1093/hmg/ddr170.
Article
CAS
PubMed
Google Scholar
Liang P, Song F, Ghosh S, Morien E, Qin M, Mahmood S, et al. Genome-wide survey reveals dynamic widespread tissue-specific changes in DNA methylation during development. BMC Genomics. 2011;12(1):231. doi:10.1186/1471-2164-12-231.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009;462(7271):315–22. doi:10.1038/nature08514.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ji H, Ehrlich LI, Seita J, Murakami P, Doi A, Lindau P, et al. Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature. 2010;467(7313):338–42. doi:10.1038/nature09367.
Article
CAS
PubMed
PubMed Central
Google Scholar
Laurent L, Wong E, Li G, Huynh T, Tsirigos A, Ong CT, et al. Dynamic changes in the human methylome during differentiation. Genome Research. 2010;20(3):320–31. doi:10.1101/gr.101907.109.
Article
CAS
PubMed
PubMed Central
Google Scholar
Isagawa T, Nagae G, Shiraki N, Fujita T, Sato N, Ishikawa S, et al. DNA methylation profiling of embryonic stem cell differentiation into the three germ layers. PLoS One. 2011;6(10):e26052. doi:10.1371/journal.pone.0026052.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell. 2013;153(5):1134–48. doi:10.1016/j.cell.2013.04.022.
Article
CAS
PubMed
PubMed Central
Google Scholar
Carrio E, Diez-Villanueva A, Lois S, Mallona I, Cases I, Forn M, et al. Deconstruction of DNA methylation patterns during myogenesis reveals specific epigenetic events in the establishment of the skeletal muscle lineage. Stem Cells. 2015;10:2015.
Google Scholar
Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science. 2009;324(5929):930–5. doi:10.1126/science.1170116.
Article
CAS
PubMed
PubMed Central
Google Scholar
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(7310):1129. 33.
Article
CAS
PubMed
PubMed Central
Google Scholar
Morgan HD, Dean W, Coker HA, Reik W, Petersen-Mahrt SK. Activation-induced cytidine deaminase deaminates 5-methylcytosine in DNA and is expressed in pluripotent tissues: implications for epigenetic reprogramming. J Biol Chem. 2004;279(50):52353–60.
Article
CAS
PubMed
Google Scholar
Bhutani N, Brady JJ, Damian M, Sacco A, Corbel SY, Blau HM. Reprogramming towards pluripotency requires AID-dependent DNA demethylation. Nature. 2010;463(7284):1042–7. doi:10.1038/nature08752.
Article
CAS
PubMed
PubMed Central
Google Scholar
Guo JU, Su Y, Zhong C, Ming GL, Song H. Emerging roles of TET proteins and 5-hydroxymethylcytosines in active DNA demethylation and beyond. Cell Cycle. 2011;10(16):2662–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang F, Pomerantz JH, Sen G, Palermo AT, Blau HM. Active tissue-specific DNA demethylation conferred by somatic cell nuclei in stable heterokaryons. Proc Natl Acad Sci U S A. 2007;104(11):4395–400. doi:10.1073/pnas.0700181104.
Article
CAS
PubMed
PubMed Central
Google Scholar
Garcia-Prat L, Sousa-Victor P, Munoz-Canoves P. Functional dysregulation of stem cells during aging: a focus on skeletal muscle stem cells. FEBS J. 2013;280(17):4051–62. doi:10.1111/febs.12221.
Article
CAS
PubMed
Google Scholar
Buckingham M, Rigby PW. Gene regulatory networks and transcriptional mechanisms that control myogenesis. Dev Cell. 2014;28(3):225–38.
Article
CAS
PubMed
Google Scholar
Kassar-Duchossoy L, Giacone E, Gayraud-Morel B, Jory A, Gomes D, Tajbakhsh S. Pax3/Pax7 mark a novel population of primitive myogenic cells during development. Genes Dev. 2005;19(12):1426–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Relaix F, Rocancourt D, Mansouri A, Buckingham M. A Pax3/Pax7-dependent population of skeletal muscle progenitor cells. Nature. 2005;435(7044):948–53. doi:10.1038/nature03594.
Article
CAS
PubMed
Google Scholar
Seale P, Sabourin LA, Girgis-Gabardo A, Mansouri A, Gruss P, Rudnicki MA. Pax7 is required for the specification of myogenic satellite cells. Cell. 2000;102(6):777–86.
Article
CAS
PubMed
Google Scholar
Jones PA, Wolkowicz MJ, Rideout WM, Gonzales FA, Marziasz CM, Coetzee GA, et al. De novo methylation of the MyoD1 CpG island during the establishment of immortal cell lines. Proc Natl Acad Sci USA. 1990;87(16):6117–21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bird AP. CpG-rich islands and the function of DNA methylation. Nature. 1986;321(6067):209–13.
Article
CAS
PubMed
Google Scholar
Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol. 1987;196(2):261–82.
Article
CAS
PubMed
Google Scholar
Illingworth RS, Bird AP. CpG islands--'a rough guide'. FEBS Lett. 2009;583(11):1713–20. doi:10.1016/j.febslet.2009.04.012.
Article
CAS
PubMed
Google Scholar
Brunk BP, Goldhamer DJ, Emerson Jr CP. Regulated demethylation of the myoD distal enhancer during skeletal myogenesis. Dev Biol. 1996;177(2):490–503.
Article
CAS
PubMed
Google Scholar
Chen JC, Love CM, Goldhamer DJ. Two upstream enhancers collaborate to regulate the spatial patterning and timing of MyoD transcription during mouse development. Dev Dyn. 2001;221(3):274–88.
Article
CAS
PubMed
Google Scholar
Chen JC, Ramachandran R, Goldhamer DJ. Essential and redundant functions of the MyoD distal regulatory region revealed by targeted mutagenesis. Dev Biol. 2002;245(1):213–23.
Article
CAS
PubMed
Google Scholar
Brown CB, Engleka KA, Wenning J, Min Lu M, Epstein JA. Identification of a hypaxial somite enhancer element regulating Pax3 expression in migrating myoblasts and characterization of hypaxial muscle Cre transgenic mice. Genesis. 2005;41(4):202–9. doi:10.1002/gene.20116.
Article
CAS
PubMed
Google Scholar
Wen Y, Bi P, Liu W, Asakura A, Keller C, Kuang S. Constitutive Notch activation upregulates Pax7 and promotes the self-renewal of skeletal muscle satellite cells. Mol Cell Biol. 2012;32(12):2300–11. doi:10.1128/MCB.06753-11.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dunham I. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57–74.
Article
CAS
Google Scholar
Blum R, Vethantham V, Bowman C, Rudnicki M, Dynlacht BD. Genome-wide identification of enhancers in skeletal muscle: the role of MyoD1. Genes Dev. 2012;26(24):763–79.
Article
Google Scholar
Azuara V, Perry P, Sauer S, Spivakov M, Jorgensen HF, John RM, et al. Chromatin signatures of pluripotent cell lines. Nat Cell Biol. 2006;8(5):532–8.
Article
CAS
PubMed
Google Scholar
Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell. 2006;125(2):315–26.
Article
CAS
PubMed
Google Scholar
Darabi R, Santos FN, Filareto A, Pan W, Koene R, Rudnicki MA, et al. Assessment of the myogenic stem cell compartment following transplantation of Pax3/Pax7-induced embryonic stem cell-derived progenitors. Stem Cells. 2011;29(5):777–90. doi:10.1002/stem.625.
Article
CAS
PubMed
PubMed Central
Google Scholar
Carrio E, Suelves M. DNA methylation dynamics in muscle development and disease. Front Aging Neurosci. 2015;5(7):19. doi:10.3389/fnagi.2015.00019.
Google Scholar
Mohn F, Weber M, Rebhan M, Roloff TC, Richter J, Stadler MB, et al. Lineage-Specific Polycomb Targets and De Novo DNA Methylation Define Restriction and Potential of Neuronal Progenitors. Molecular Cell. 2008;30(6):755–66. doi:10.1016/j.molcel.2008.05.007.
Article
CAS
PubMed
Google Scholar
Brunner AL, Johnson DS, Kim SW, Valouev A, Reddy TE, Neff NF, et al. Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Research. 2009;19(6):1044–56. doi:10.1101/gr.088773.108.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bock C, Beerman I, Lien WH, Smith ZD, Gu H, Boyle P, et al. DNA methylation dynamics during in vivo differentiation of blood and skin stem cells. Mol Cell. 2012;47(4):633–47. doi:10.1016/j.molcel.2012.06.019.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gilsbach R, Preissl S, Gruning BA, Schnick T, Burger L, Benes V, et al. Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease. Nat Commun. 2014;5:5288.
Article
CAS
PubMed
PubMed Central
Google Scholar
Palacios D, Mozzetta C, Consalvi S, Caretti G, Saccone V, Proserpio V, et al. TNF/p38α/Polycomb Signaling to Pax7 Locus in Satellite Cells Links Inflammation to the Epigenetic Control of Muscle Regeneration. Cell Stem Cell. 2010;7(4):455–69. doi:10.1016/j.stem.2010.08.013.
Article
CAS
PubMed
PubMed Central
Google Scholar
Oikawa Y, Omori R, Nishii T, Ishida Y, Kawaichi M, Matsuda E. The methyl-CpG-binding protein CIBZ suppresses myogenic differentiation by directly inhibiting myogenin expression. Cell Res. 2011. doi:10.1038/cr.2011.90.
Caretti G, Di Padova M, Micales B, Lyons GE, Sartorelli V. The Polycomb Ezh2 methyltransferase regulates muscle gene expression and skeletal muscle differentiation. Genes Dev. 2004;18(21):2627–38. doi:10.1101/gad.1241904.
Article
CAS
PubMed
PubMed Central
Google Scholar
Seenundun S, Rampalli S, Liu Q-C, Aziz A, Palii C, Hong S, et al. UTX mediates demethylation of H3K27me3 at muscle-specific genes during myogenesis. The EMBO Journal. 2010;29(8):1401–11. doi:10.1038/emboj.2010.37.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gifford CA, Ziller MJ, Gu H, Trapnell C, Donaghey J, Tsankov A, et al. Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell. 2013;153(5):1149–63. doi:10.1016/j.cell.2013.04.037.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang W, Behringer RR, Olson EN. Inactivation of the myogenic bHLH gene MRF4 results in up-regulation of myogenin and rib anomalies. Genes Dev. 1995;9(11):1388–99.
Article
CAS
PubMed
Google Scholar
Arnold HH, Braun T. Genetics of muscle determination and development. Curr Top Dev Biol. 2000;48:129–64.
Article
CAS
PubMed
Google Scholar
Sambasivan R, Comai G, Le Roux I, Gomes D, Konge J, Dumas G, et al. Embryonic founders of adult muscle stem cells are primed by the determination gene Mrf4. Dev Biol. 2013;381(1):241–55. doi:10.1016/j.ydbio.2013.04.018.
Article
CAS
PubMed
Google Scholar
Buckingham M, Relaix F. The Role ofPaxGenes in the Development of Tissues and Organs:Pax3andPax7Regulate Muscle Progenitor Cell Functions. Annual Review of Cell and Developmental Biology. 2007;23(1):645–73. doi:10.1146/annurev.cellbio.23.090506.123438.
Article
CAS
PubMed
Google Scholar
Soleimani VD, Punch VG, Kawabe Y, Jones AE, Palidwor GA, Porter CJ, et al. Transcriptional dominance of Pax7 in adult myogenesis is due to high-affinity recognition of homeodomain motifs. Dev Cell. 2012;22(6):1208–20. doi:10.1016/j.devcel.2012.03.014.
Article
CAS
PubMed
PubMed Central
Google Scholar
McKinnell IW, Ishibashi J, Le Grand F, Punch VG, Addicks GC, Greenblatt JF, et al. Pax7 activates myogenic genes by recruitment of a histone methyltransferase complex. Nat Cell Biol. 2008;10(1):77–84. doi:10.1038/ncb1671.
Article
CAS
PubMed
PubMed Central
Google Scholar
Simone C, Forcales SV, Hill DA, Imbalzano AN, Latella L, Puri PL. p38 pathway targets SWI-SNF chromatin-remodeling complex to muscle-specific loci. Nat Genet. 2004;36(7):738–43. doi:10.1038/ng1378.
Article
CAS
PubMed
Google Scholar
de la Serna IL, Ohkawa Y, Berkes CA, Bergstrom DA, Dacwag CS, Tapscott SJ, et al. MyoD targets chromatin remodeling complexes to the myogenin locus prior to forming a stable DNA-bound complex. Mol Cell Biol. 2005;25(10):3997–4009.
Article
PubMed
PubMed Central
Google Scholar
Puri PL, Sartorelli V, Yang XJ, Hamamori Y, Ogryzko VV, Howard BH, et al. Differential roles of p300 and PCAF acetyltransferases in muscle differentiation. Mol Cell. 1997;1(1):35–45.
Article
CAS
PubMed
Google Scholar
Cao Y, Yao Z, Sarkar D, Lawrence M, Sanchez GJ, Parker MH, et al. Genome-wide MyoD Binding in Skeletal Muscle Cells: A Potential for Broad Cellular Reprogramming. Developmental Cell. 2010;18(4):662–74. doi:10.1016/j.devcel.2010.02.014.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mozzetta C, Consalvi S, Saccone V, Forcales SV, Puri PL, Palacios D. Selective control of Pax7 expression by TNF-activated p38alpha/polycomb repressive complex 2 (PRC2) signaling during muscle satellite cell differentiation. Cell Cycle. 2011;10(2):191–8.
Article
CAS
PubMed
Google Scholar
Liao W, Hong SH, Chan BH, Rudolph FB, Clark SC, Chan L. APOBEC-2, a cardiac- and skeletal muscle-specific member of the cytidine deaminase supergene family. Biochem Biophys Res Commun. 1999;260(2):398–404.
Article
CAS
PubMed
Google Scholar
Anant S, Mukhopadhyay D, Sankaranand V, Kennedy S, Henderson JO, Davidson NO. ARCD-1, an apobec-1-related cytidine deaminase, exerts a dominant negative effect on C to U RNA editing. Am J Physiol Cell Physiol. 2001;281(6):C1904–16.
CAS
PubMed
Google Scholar
Mikl MC, Watt IN, Lu M, Reik W, Davies SL, Neuberger MS, et al. Mice deficient in APOBEC2 and APOBEC3. Mol Cell Biol. 2005;25(16):7270–7. doi:10.1128/MCB.25.16.7270-7277.2005.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sato Y, Probst HC, Tatsumi R, Ikeuchi Y, Neuberger MS, Rada C. Deficiency in APOBEC2 leads to a shift in muscle fiber type, diminished body mass, and myopathy. J Biol Chem. 2010;285(10):7111–8. doi:10.1074/jbc.M109.052977.
Article
CAS
PubMed
PubMed Central
Google Scholar
Harris RS, Petersen-Mahrt SK, Neuberger MS. RNA editing enzyme APOBEC1 and some of its homologs can act as DNA mutators. Mol Cell. 2002;10(5):1247–53.
Article
CAS
PubMed
Google Scholar
Lada AG, Krick CF, Kozmin SG, Mayorov VI, Karpova TS, Rogozin IB, et al. Mutator effects and mutation signatures of editing deaminases produced in bacteria and yeast. Biochemistry. 2011;76(1):131–46.
CAS
PubMed
PubMed Central
Google Scholar
Nabel CS, Jia H, Ye Y, Shen L, Goldschmidt HL, Stivers JT, et al. AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation. Nat Chem Biol. 2012;8(9):751–8. doi:10.1038/nchembio.42.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rai K, Huggins IJ, James SR, Karpf AR, Jones DA, Cairns BR. DNA demethylation in zebrafish involves the coupling of a deaminase, a glycosylase, and gadd45. Cell. 2008;135(7):1201–12. doi:10.1016/j.cell.2008.11.042.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vonica A, Rosa A, Arduini BL, Brivanlou AH. APOBEC2, a selective inhibitor of TGFbeta signaling, regulates left-right axis specification during early embryogenesis. Dev Biol. 2011;350(1):13–23. doi:10.1016/j.ydbio.2010.09.016.
Article
CAS
PubMed
PubMed Central
Google Scholar
Powell C, Elsaeidi F, Goldman D. Injury-dependent Muller glia and ganglion cell reprogramming during tissue regeneration requires Apobec2a and Apobec2b. J Neurosci. 2012;32(3):1096–109.
Article
CAS
PubMed
PubMed Central
Google Scholar
Powell C, Grant AR, Cornblath E, Goldman D. Analysis of DNA methylation reveals a partial reprogramming of the Muller glia genome during retina regeneration. Proc Natl Acad Sci U S A. 2013;110(49):19814–9. doi:10.1073/pnas.1312009110.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rudnicki MA, Schnegelsberg PN, Stead RH, Braun T, Arnold HH, Jaenisch R. MyoD or Myf-5 is required for the formation of skeletal muscle. Cell. 1993;75(7):1351–9.
Article
CAS
PubMed
Google Scholar
Suelves M, Vidal B, Serrano AL, Tjwa M, Roma J, Lopez-Alemany R, et al. uPA deficiency exacerbates muscular dystrophy in MDX mice. J Cell Biol. 2007;178(6):1039–51. doi:10.1083/jcb.200705127.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jozefczuk J, Drews K, Adjaye J. Preparation of mouse embryonic fibroblast cells suitable for culturing human embryonic and induced pluripotent stem cells. J Vis Exp. 2012;21:(64.
Google Scholar
Follenzi A, Ailles LE, Bakovic S, Geuna M, Naldini L. Gene transfer by lentiviral vectors is limited by nuclear translocation and rescued by HIV-1 pol sequences. Nat Genet. 2000;25(2):217–22.
Article
CAS
PubMed
Google Scholar
Clark SJ, Statham A, Stirzaker C, Molloy PL, Frommer M. DNA methylation: bisulphite modification and analysis. Nat Protoc. 2006;1(5):2353–64.
Article
CAS
PubMed
Google Scholar
Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29(1):24–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mallona I, Diez-Villanueva A, Peinado MA. Methylation plotter: a web tool for dynamic visualization of DNA methylation data. Source Code Biol Med. 2014;7(9):11. doi:10.1186/751-0473-9-11.
Article
Google Scholar