Early de novo DNA methylation and prolonged demethylation in the muscle lineage

References

• Ehrlich M, Gama-Sosa MA, Huang L-H, Midgett RM, Kuo KC, McCune RA, et al. Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells. Nucleic Acids Res 1982; 10:2709 - 21; http://dx.doi.org/10.1093/nar/10.8.2709; PMID: 7079182
   PubMed Web of Science ®Google Scholar
• Ndlovu MN, Denis H, Fuks F. Exposing the DNA methylome iceberg. Trends Biochem Sci 2011; 36:381 - 7; PMID: 21497094
   PubMed Web of Science ®Google Scholar
• Kriaucionis S, Heintz N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 2009; 324:929 - 30; http://dx.doi.org/10.1126/science.1169786; PMID: 19372393
   PubMed Web of Science ®Google Scholar
• Ficz G, Branco MR, Seisenberger S, Santos F, Krueger F, Hore TA, et al. Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature 2011; 473:398 - 402; http://dx.doi.org/10.1038/nature10008; PMID: 21460836
   PubMed Web of Science ®Google Scholar
• Guo JU, Su Y, Zhong C, Ming GL, Song H. Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell 2011; 145:423 - 34; http://dx.doi.org/10.1016/j.cell.2011.03.022; PMID: 21496894
   PubMed Web of Science ®Google Scholar
• Jin SG, Wu X, Li AX, Pfeifer GP. Genomic mapping of 5-hydroxymethylcytosine in the human brain. Nucleic Acids Res 2011; 39:5015 - 24; http://dx.doi.org/10.1093/nar/gkr120; PMID: 21378125
   PubMed Web of Science ®Google Scholar
• Hashimoto H, Vertino PM, Cheng X. Molecular coupling of DNA methylation and histone methylation. Epigenomics 2010; 2:657 - 69; http://dx.doi.org/10.2217/epi.10.44; PMID: 21339843
   PubMed Web of Science ®Google Scholar
• Cotton AM, Lam L, Affleck JG, Wilson IM, Peñaherrera MS, McFadden DE, et al. Chromosome-wide DNA methylation analysis predicts human tissue-specific X inactivation. Hum Genet 2011; 130:187 - 201; http://dx.doi.org/10.1007/s00439-011-1007-8; PMID: 21597963
   PubMed Web of Science ®Google Scholar
• Yuen RK, Neumann SM, Fok AK, Peñaherrera MS, McFadden DE, Robinson WP, et al. Extensive epigenetic reprogramming in human somatic tissues between fetus and adult. Epigenetics Chromatin 2011; 4:7; http://dx.doi.org/10.1186/1756-8935-4-7; PMID: 21545704
   PubMed Web of Science ®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:e26052; http://dx.doi.org/10.1371/journal.pone.0026052; PMID: 22016810
   PubMedGoogle Scholar
• Berdasco M, Melguizo C, Prados J, Gómez A, Alaminos M, Pujana MA, et al. DNA methylation plasticity of human adipose-derived stem cells in lineage commitment. Am J Pathol 2012; 181:2079 - 93; http://dx.doi.org/10.1016/j.ajpath.2012.08.016; PMID: 23031258
   PubMed Web of Science ®Google Scholar
• Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 2008; 454:766 - 70; PMID: 18600261
   PubMed Web of Science ®Google Scholar
• Tsumagari K, Chang S-C, Lacey M, Baribault C, Chittur SV, Sowden J, et al. Gene expression during normal and FSHD myogenesis. BMC Med Genomics 2011; 4:67; http://dx.doi.org/10.1186/1755-8794-4-67; PMID: 21951698
   PubMed Web of Science ®Google Scholar
• 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; http://dx.doi.org/10.1371/journal.pone.0015367; PMID: 21203455
   PubMed Web of Science ®Google Scholar
• Jin SG, Jiang Y, Qiu R, Rauch TA, Wang Y, Schackert G, et al. 5-Hydroxymethylcytosine is strongly depleted in human cancers but its levels do not correlate with IDH1 mutations. Cancer Res 2011; 71:7360 - 5; http://dx.doi.org/10.1158/0008-5472.CAN-11-2023; PMID: 22052461
   PubMed Web of Science ®Google Scholar
• Terragni J, Bitinaite J, Zheng Y, Pradhan S. Biochemical characterization of recombinant β-glucosyltransferase and analysis of global 5-hydroxymethylcytosine in unique genomes. Biochemistry 2012; 51:1009 - 19; http://dx.doi.org/10.1021/bi2014739; PMID: 22229759
   PubMed Web of Science ®Google Scholar
• Collins CA, Gnocchi VF, White RB, Boldrin L, Perez-Ruiz A, Relaix F, et al. Integrated functions of Pax3 and Pax7 in the regulation of proliferation, cell size and myogenic differentiation. PLoS One 2009; 4:e4475; http://dx.doi.org/10.1371/journal.pone.0004475; PMID: 19221588
   PubMed Web of Science ®Google Scholar
• Medic S, Rizos H, Ziman M. Differential PAX3 functions in normal skin melanocytes and melanoma cells. Biochem Biophys Res Commun 2011; 411:832 - 7; http://dx.doi.org/10.1016/j.bbrc.2011.07.053; PMID: 21802410
   PubMed Web of Science ®Google Scholar
• Pane LS, Zhang Z, Ferrentino R, Huynh T, Cutillo L, Baldini A. Tbx1 is a negative modulator of Mef2c. Hum Mol Genet 2012; 21:2485 - 96; http://dx.doi.org/10.1093/hmg/dds063; PMID: 22367967
   PubMed Web of Science ®Google Scholar
• Xu YJ, Wang J, Xu R, Zhao PJ, Wang XK, Sun HJ, et al. Detecting 22q11.2 deletion in Chinese children with conotruncal heart defects and single nucleotide polymorphisms in the haploid TBX1 locus. BMC Med Genet 2011; 12:169; http://dx.doi.org/10.1186/1471-2350-12-169; PMID: 22185286
   PubMed Web of Science ®Google Scholar
• Bell ML, Buvoli M, Leinwand LA. Uncoupling of expression of an intronic microRNA and its myosin host gene by exon skipping. Mol Cell Biol 2010; 30:1937 - 45; http://dx.doi.org/10.1128/MCB.01370-09; PMID: 20154144
   PubMed Web of Science ®Google Scholar
• Shieh JT, Huang Y, Gilmore J, Srivastava D. Elevated miR-499 levels blunt the cardiac stress response. PLoS One 2011; 6:e19481; http://dx.doi.org/10.1371/journal.pone.0019481; PMID: 21573063
   PubMed Web of Science ®Google Scholar
• Kontrogianni-Konstantopoulos A, Ackermann MA, Bowman AL, Yap SV, Bloch RJ. Muscle giants: molecular scaffolds in sarcomerogenesis. Physiol Rev 2009; 89:1217 - 67; http://dx.doi.org/10.1152/physrev.00017.2009; PMID: 19789381
   PubMed Web of Science ®Google Scholar
• Branciamore S, Chen ZX, Riggs AD, Rodin SN. CpG island clusters and pro-epigenetic selection for CpGs in protein-coding exons of HOX and other transcription factors. Proc Natl Acad Sci U S A 2010; 107:15485 - 90; http://dx.doi.org/10.1073/pnas.1010506107; PMID: 20716685
   PubMed Web of Science ®Google Scholar
• McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, et al. GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol 2010; 28:495 - 501; http://dx.doi.org/10.1038/nbt.1630; PMID: 20436461
   PubMed Web of Science ®Google Scholar
• Dastjerdi A, Robson L, Walker R, Hadley J, Zhang Z, Rodriguez-Niedenführ M, et al. Tbx1 regulation of myogenic differentiation in the limb and cranial mesoderm. Dev Dyn 2007; 236:353 - 63; http://dx.doi.org/10.1002/dvdy.21010; PMID: 17117436
   PubMed Web of Science ®Google Scholar
• Havis E, Coumailleau P, Bonnet A, Bismuth K, Bonnin MA, Johnson R, et al. Sim2 prevents entry into the myogenic program by repressing MyoD transcription during limb embryonic myogenesis. Development 2012; 139:1910 - 20; http://dx.doi.org/10.1242/dev.072561; PMID: 22513369
   PubMed Web of Science ®Google Scholar
• Ehrlich M, Lacey M. Deciphering transcription dysregulation in FSH muscular dystrophy. J Hum Genet 2012; 57:477 - 84; http://dx.doi.org/10.1038/jhg.2012.74; PMID: 22718021
   PubMed Web of Science ®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; 10:2662 - 8; http://dx.doi.org/10.4161/cc.10.16.17093; PMID: 21811096
   PubMed Web of Science ®Google Scholar
• Kang JS, Krauss RS. Muscle stem cells in developmental and regenerative myogenesis. Curr Opin Clin Nutr Metab Care 2010; 13:243 - 8; http://dx.doi.org/10.1097/MCO.0b013e328336ea98; PMID: 20098319
   PubMed Web of Science ®Google Scholar
• Milewski RC, Chi NC, Li J, Brown C, Lu MM, Epstein JA. Identification of minimal enhancer elements sufficient for Pax3 expression in neural crest and implication of Tead2 as a regulator of Pax3. Development 2004; 131:829 - 37; http://dx.doi.org/10.1242/dev.00975; PMID: 14736747
   PubMed Web of Science ®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; 41:202 - 9; http://dx.doi.org/10.1002/gene.20116; PMID: 15789408
   PubMed Web of Science ®Google Scholar
• Degenhardt KR, Milewski RC, Padmanabhan A, Miller M, Singh MK, Lang D, et al. Distinct enhancers at the Pax3 locus can function redundantly to regulate neural tube and neural crest expressions. Dev Biol 2010; 339:519 - 27; http://dx.doi.org/10.1016/j.ydbio.2009.12.030; PMID: 20045680
   PubMed Web of Science ®Google Scholar
• Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010; 28:511 - 5; http://dx.doi.org/10.1038/nbt.1621; PMID: 20436464
   PubMed Web of Science ®Google Scholar
• Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008; 5:621 - 8; http://dx.doi.org/10.1038/nmeth.1226; PMID: 18516045
   PubMed Web of Science ®Google Scholar
• Tsukamoto K, Nakamura Y, Niikawa N. Isolation of two isoforms of the PAX3 gene transcripts and their tissue-specific alternative expression in human adult tissues. Hum Genet 1994; 93:270 - 4; http://dx.doi.org/10.1007/BF00212021; PMID: 7545913
   PubMed Web of Science ®Google Scholar
• Roth RB, Hevezi P, Lee J, Willhite D, Lechner SM, Foster AC, et al. Gene expression analyses reveal molecular relationships among 20 regions of the human CNS. Neurogenetics 2006; 7:67 - 80; http://dx.doi.org/10.1007/s10048-006-0032-6; PMID: 16572319
   PubMed Web of Science ®Google Scholar
• Wu C, Orozco C, Boyer J, Leglise M, Goodale J, Batalov S, et al. BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol 2009; 10:R130; http://dx.doi.org/10.1186/gb-2009-10-11-r130; PMID: 19919682
   PubMed Web of Science ®Google Scholar
• Cortese R, Krispin M, Weiss G, Berlin K, Eckhardt F. DNA methylation profiling of pseudogene-parental gene pairs and two gene families. Genomics 2008; 91:492 - 502; http://dx.doi.org/10.1016/j.ygeno.2008.02.004; PMID: 18450418
   PubMed Web of Science ®Google Scholar
• Wagner EJ, Carpenter PB. Understanding the language of Lys36 methylation at histone H3. Nat Rev Mol Cell Biol 2012; 13:115 - 26; http://dx.doi.org/10.1038/nrm3274; PMID: 22266761
   PubMed Web of Science ®Google Scholar
• Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, et al. High-resolution mapping and characterization of open chromatin across the genome. Cell 2008; 132:311 - 22; http://dx.doi.org/10.1016/j.cell.2007.12.014; PMID: 18243105
   PubMed Web of Science ®Google Scholar
• Paylor R, Glaser B, Mupo A, Ataliotis P, Spencer C, Sobotka A, et al. Tbx1 haploinsufficiency is linked to behavioral disorders in mice and humans: implications for 22q11 deletion syndrome. Proc Natl Acad Sci U S A 2006; 103:7729 - 34; http://dx.doi.org/10.1073/pnas.0600206103; PMID: 16684884
   PubMed Web of Science ®Google Scholar
• Zlatanova J, Caiafa P. CCCTC-binding factor: to loop or to bridge. Cell Mol Life Sci 2009; 66:1647 - 60; http://dx.doi.org/10.1007/s00018-009-8647-z; PMID: 19137260
   PubMed Web of Science ®Google Scholar
• Myers RM, Stamatoyannopoulos J, Snyder M, Dunham I, Hardison RC, Bernstein BE, et al, ENCODE Project Consortium. A user’s guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 2011; 9:e1001046; http://dx.doi.org/10.1371/journal.pbio.1001046; PMID: 21526222
   PubMed Web of Science ®Google Scholar
• Russell MW, Raeker MO, Korytkowski KA, Sonneman KJ. Identification, tissue expression and chromosomal localization of human Obscurin-MLCK, a member of the titin and Dbl families of myosin light chain kinases. Gene 2002; 282:237 - 46; http://dx.doi.org/10.1016/S0378-1119(01)00795-8; PMID: 11814696
   PubMed Web of Science ®Google Scholar
• Rubio MD, Johnson R, Miller CA, Huganir RL, Rumbaugh G. Regulation of synapse structure and function by distinct myosin II motors. J Neurosci 2011; 31:1448 - 60; http://dx.doi.org/10.1523/JNEUROSCI.3294-10.2011; PMID: 21273429
   PubMed Web of Science ®Google Scholar
• van Rooij E, Quiat D, Johnson BA, Sutherland LB, Qi X, Richardson JA, et al. A family of microRNAs encoded by myosin genes governs myosin expression and muscle performance. Dev Cell 2009; 17:662 - 73; http://dx.doi.org/10.1016/j.devcel.2009.10.013; PMID: 19922871
   PubMed Web of Science ®Google Scholar
• Young P, Ehler E, Gautel M. Obscurin, a giant sarcomeric Rho guanine nucleotide exchange factor protein involved in sarcomere assembly. J Cell Biol 2001; 154:123 - 36; http://dx.doi.org/10.1083/jcb.200102110; PMID: 11448995
   PubMed Web of Science ®Google Scholar
• Branco MR, Ficz G, Reik W. Uncovering the role of 5-hydroxymethylcytosine in the epigenome. Nat Rev Genet 2012; 13:7 - 13; PMID: 22083101
   PubMed Web of Science ®Google Scholar
• Zhang L, Lu X, Lu J, Liang H, Dai Q, Xu GL, et al. Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA. Nat Chem Biol 2012; 8:328 - 30; http://dx.doi.org/10.1038/nchembio.914; PMID: 22327402
   PubMed Web of Science ®Google Scholar
• Hackett JA, Zylicz JJ, Surani MA. Parallel mechanisms of epigenetic reprogramming in the germline. Trends Genet 2012; 28:164 - 74; http://dx.doi.org/10.1016/j.tig.2012.01.005; PMID: 22386917
   PubMed Web of Science ®Google Scholar
• He YF, Li BZ, 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; http://dx.doi.org/10.1126/science.1210944; PMID: 21817016
   PubMed Web of Science ®Google Scholar
• Cortellino S, Xu J, Sannai M, Moore R, Caretti E, Cigliano A, et al. Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair. Cell 2011; 146:67 - 79; http://dx.doi.org/10.1016/j.cell.2011.06.020; PMID: 21722948
   PubMed Web of Science ®Google Scholar
• Rangam G, Schmitz KM, Cobb AJ, Petersen-Mahrt SK. AID enzymatic activity is inversely proportional to the size of cytosine C5 orbital cloud. PLoS One 2012; 7:e43279; http://dx.doi.org/10.1371/journal.pone.0043279; PMID: 22916236
   PubMedGoogle Scholar
• Ono R, Taki T, Taketani T, Taniwaki M, Kobayashi H, Hayashi Y. LCX, leukemia-associated protein with a CXXC domain, is fused to MLL in acute myeloid leukemia with trilineage dysplasia having t(10;11)(q22;q23). Cancer Res 2002; 62:4075 - 80; PMID: 12124344
   PubMed Web of Science ®Google Scholar
• Tang H, Araki K, Li Z, Yamamura K. Characterization of Ayu17-449 gene expression and resultant kidney pathology in a knockout mouse model. Transgenic Res 2008; 17:599 - 608; http://dx.doi.org/10.1007/s11248-008-9170-y; PMID: 18288583
   PubMed Web of Science ®Google Scholar
• Hashimoto H, Liu Y, Upadhyay AK, Chang Y, Howerton SB, Vertino PM, et al. Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation. Nucleic Acids Res 2012; 40:4841 - 9; http://dx.doi.org/10.1093/nar/gks155; PMID: 22362737
   PubMed Web of Science ®Google Scholar
• Chieffo C, Garvey N, Gong W, Roe B, Zhang G, Silver L, et al. Isolation and characterization of a gene from the DiGeorge chromosomal region homologous to the mouse Tbx1 gene. Genomics 1997; 43:267 - 77; http://dx.doi.org/10.1006/geno.1997.4829; PMID: 9268629
   PubMed Web of Science ®Google Scholar
• Bocker MT, Tuorto F, Raddatz G, Musch T, Yang FC, Xu M, et al. Hydroxylation of 5-methylcytosine by TET2 maintains the active state of the mammalian HOXA cluster. Nat Commun 2012; 3:818; http://dx.doi.org/10.1038/ncomms1826; PMID: 22569366
   PubMed Web of Science ®Google Scholar
• Sérandour AA, Avner S, Oger F, Bizot M, Percevault F, Lucchetti-Miganeh C, et al. Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers. Nucleic Acids Res 2012; 40:8255 - 65; http://dx.doi.org/10.1093/nar/gks595; PMID: 22730288
   PubMed Web of Science ®Google Scholar
• Shukla S, Kavak E, Gregory M, Imashimizu M, Shutinoski B, Kashlev M, et al. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature 2011; 479:74 - 9; http://dx.doi.org/10.1038/nature10442; PMID: 21964334
   PubMed Web of Science ®Google Scholar
• Khare T, Pai S, Koncevicius K, Pal M, Kriukiene E, Liutkeviciute Z, et al. 5-hmC in the brain is abundant in synaptic genes and shows differences at the exon-intron boundary. Nat Struct Mol Biol 2012; 19:1037 - 43; http://dx.doi.org/10.1038/nsmb.2372; PMID: 22961382
   PubMed Web of Science ®Google Scholar
• Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 2011; 473:43 - 9; http://dx.doi.org/10.1038/nature09906; PMID: 21441907
   PubMed Web of Science ®Google Scholar
• Pekowska A, Benoukraf T, Zacarias-Cabeza J, Belhocine M, Koch F, Holota H, et al. H3K4 tri-methylation provides an epigenetic signature of active enhancers. EMBO J 2011; 30:4198 - 210; http://dx.doi.org/10.1038/emboj.2011.295; PMID: 21847099
   PubMed Web of Science ®Google Scholar
• Zhang Z, Baldini A. Manipulation of endogenous regulatory elements and transgenic analyses of the Tbx1 gene. Mamm Genome 2010; 21:556 - 64; http://dx.doi.org/10.1007/s00335-010-9304-4; PMID: 21107579
   PubMed Web of Science ®Google Scholar
• Simrick S, Szumska D, Gardiner JR, Jones K, Sagar K, Morrow B, et al. Biallelic expression of Tbx1 protects the embryo from developmental defects caused by increased receptor tyrosine kinase signaling. Dev Dyn 2012; 241:1310 - 24; http://dx.doi.org/10.1002/dvdy.23812; PMID: 22674535
   PubMed Web of Science ®Google Scholar
• Wang J, Greene SB, Bonilla-Claudio M, Tao Y, Zhang J, Bai Y, et al. Bmp signaling regulates myocardial differentiation from cardiac progenitors through a MicroRNA-mediated mechanism. Dev Cell 2010; 19:903 - 12; http://dx.doi.org/10.1016/j.devcel.2010.10.022; PMID: 21145505
   PubMed Web of Science ®Google Scholar
• Booth MJ, Branco MR, Ficz G, Oxley D, Krueger F, Reik W, et al. Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science 2012; 336:934 - 7; http://dx.doi.org/10.1126/science.1220671; PMID: 22539555
   PubMed Web of Science ®Google Scholar
• Brown SJ, Stoilov P, Xing Y. Chromatin and epigenetic regulation of pre-mRNA processing. Hum Mol Genet 2012; 21:R1 R90 - 6; http://dx.doi.org/10.1093/hmg/dds353; PMID: 22936691
   PubMedGoogle Scholar
• de Wilde J, Hulshof MF, Boekschoten MV, de Groot P, Smit E, Mariman EC. The embryonic genes Dkk3, Hoxd8, Hoxd9 and Tbx1 identify muscle types in a diet-independent and fiber-type unrelated way. BMC Genomics 2010; 11:176; http://dx.doi.org/10.1186/1471-2164-11-176; PMID: 20230627
   PubMed Web of Science ®Google Scholar
• Greulich F, Rudat C, Kispert A. Mechanisms of T-box gene function in the developing heart. Cardiovasc Res 2011; 91:212 - 22; http://dx.doi.org/10.1093/cvr/cvr112; PMID: 21498422
   PubMed Web of Science ®Google Scholar
• Zingg JM, Pedraza-Alva G, Jost JP. MyoD1 promoter autoregulation is mediated by two proximal E-boxes. Nucleic Acids Res 1994; 22:2234 - 41; http://dx.doi.org/10.1093/nar/22.12.2234; PMID: 8036150
   PubMed Web of Science ®Google Scholar
• Fuso A, Ferraguti G, Grandoni F, Ruggeri R, Scarpa S, Strom R, et al. Early demethylation of non-CpG, CpC-rich, elements in the myogenin 5′-flanking region: a priming effect on the spreading of active demethylation. Cell Cycle 2010; 9:3965 - 76; http://dx.doi.org/10.4161/cc.9.19.13193; PMID: 20935518
   PubMed Web of Science ®Google Scholar
• Hupkes M, Jonsson MK, Scheenen WJ, van Rotterdam W, Sotoca AM, van Someren EP, et al. Epigenetics: DNA demethylation promotes skeletal myotube maturation. FASEB J 2011; 25:3861 - 72; http://dx.doi.org/10.1096/fj.11-186122; PMID: 21795504
   PubMed Web of Science ®Google Scholar
• Barrès R, Yan J, Egan B, Treebak JT, Rasmussen M, Fritz T, et al. Acute exercise remodels promoter methylation in human skeletal muscle. Cell Metab 2012; 15:405 - 11; http://dx.doi.org/10.1016/j.cmet.2012.01.001; PMID: 22405075
   PubMed Web of Science ®Google Scholar
• Gertz J, Varley KE, Reddy TE, Bowling KM, Pauli F, Parker SL, et al. Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS Genet 2011; 7:e1002228; http://dx.doi.org/10.1371/journal.pgen.1002228; PMID: 21852959
   PubMed Web of Science ®Google Scholar
• R-Development-Core-Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing. Vienna, Austria: ISBN 3-900051-07-0, 2011.
   Google Scholar
• Kane MJ, Emerson JW. bigmemory: Manage massive matrices with shared memory and memory-mapped files. 2011; http://CRAN.R-project.org/package=bigmemory.
   Google Scholar
• Bates D, Maechler M, Bolker B. lme4: Linear mixed-effects models using S4 classes. R package version 0.999375-42. 2011; http://CRAN.R-project.org/package=lme4.
   Google Scholar
• Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010; 26:841 - 2; http://dx.doi.org/10.1093/bioinformatics/btq033; PMID: 20110278
   PubMed Web of Science ®Google Scholar
• Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, et al. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res 2011; 21:1757 - 67; http://dx.doi.org/10.1101/gr.121541.111; PMID: 21750106
   PubMed Web of Science ®Google Scholar
• Shibata Y, Sheffield NC, Fedrigo O, Babbitt CC, Wortham M, Tewari AK, et al. Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection. PLoS Genet 2012; 8:e1002789; http://dx.doi.org/10.1371/journal.pgen.1002789; PMID: 22761590
   PubMedGoogle Scholar
• Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 2012; 7:562 - 78; http://dx.doi.org/10.1038/nprot.2012.016; PMID: 22383036
   PubMed Web of Science ®Google Scholar