title: Early de novo DNA methylation and prolonged demethylation in the muscle lineage.
abstract: Myogenic cell cultures derived from muscle biopsies are excellent models for human cell differentiation. We report the first comprehensive analysis of myogenesis-specific DNA hyper- and hypo-methylation throughout the genome for human muscle progenitor cells (both myoblasts and myotubes) and skeletal muscle tissue vs. 30 non-muscle samples using reduced representation bisulfite sequencing. We also focused on four genes with extensive hyper- or hypo-methylation in the muscle lineage (PAX3, TBX1, MYH7B/MIR499 and OBSCN) to compare DNA methylation, DNaseI hypersensitivity, histone modification, and CTCF binding profiles. We found that myogenic hypermethylation was strongly associated with homeobox or T-box genes and muscle hypomethylation with contractile fiber genes. Nonetheless, there was no simple relationship between differential gene expression and myogenic differential methylation, rather only for subsets of these genes, such as contractile fiber genes. Skeletal muscle retained ~30% of the hypomethylated sites but only ~3% of hypermethylated sites seen in myogenic progenitor cells. By enzymatic assays, skeletal muscle was 2-fold enriched globally in genomic 5-hydroxymethylcytosine (5-hmC) vs. myoblasts or myotubes and was the only sample type enriched in 5-hmC at tested myogenic hypermethylated sites in PAX3/CCDC140 andTBX1. TET1 and TET2 RNAs, which are involved in generation of 5-hmC and DNA demethylation, were strongly upregulated in myoblasts and myotubes. Our findings implicate de novo methylation predominantly before the myoblast stage and demethylation before and after the myotube stage in control of transcription and co-transcriptional RNA processing. They also suggest that, in muscle, TET1 or TET2 are involved in active demethylation and in formation of stable 5-hmC residues.
authors: Program in Human Genetics and Tulane Cancer Center, Tulane Health Sciences Center, New Orleans, LA, USA.
authors: Koji
authors: K
authors: Tsumagari
authors: Carl
authors: C
authors: Baribault
authors: Jolyon
authors: J
authors: Terragni
authors: Katherine E
authors: KE
authors: Varley
authors: Jason
authors: J
authors: Gertz
authors: Sirharsa
authors: S
authors: Pradhan
authors: Melody
authors: M
authors: Badoo
authors: Charlene M
authors: CM
authors: Crain
authors: Lingyun
authors: L
authors: Song
authors: Gregory E
authors: GE
authors: Crawford
authors: Richard M
authors: RM
authors: Myers
authors: Michelle
authors: M
authors: Lacey
authors: Melanie
authors: M
authors: Ehrlich
mesh_terms: D044503:5-Methylcytosine / Q000031:analogs & derivatives; D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000076246:CCCTC-Binding Factor; D024722:Cardiac Myosins / Q000235:genetics / Q000378:metabolism; D016022:Case-Control Studies; D019070:Cell Lineage / Q000235:genetics*; D002648:Child; D003596:Cytosine / Q000031:analogs & derivatives / Q000378:metabolism; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D049308:Dioxygenases; D044127:Epigenesis, Genetic; D005260:Female; D018507:Gene Expression Regulation, Developmental; D005801:Genes, Homeobox; D015894:Genome, Human; D020662:Guanine Nucleotide Exchange Factors / Q000235:genetics / Q000378:metabolism; D006657:Histones / Q000378:metabolism; D006801:Humans; D007231:Infant, Newborn; D008297:Male; D008875:Middle Aged; D006899:Mixed Function Oxygenases; D024510:Muscle Development / Q000235:genetics*; D018485:Muscle Fibers, Skeletal / Q000378:metabolism; D009124:Muscle Proteins / Q000235:genetics / Q000378:metabolism; D020391:Muscular Dystrophy, Facioscapulohumeral / Q000235:genetics* / Q000378:metabolism; D032446:Myoblasts / Q000378:metabolism; D018995:Myosin Heavy Chains / Q000235:genetics / Q000378:metabolism; D000072041:PAX3 Transcription Factor; D051761:Paired Box Transcription Factors / Q000235:genetics / Q000378:metabolism; D017346:Protein Serine-Threonine Kinases; D011518:Proto-Oncogene Proteins / Q000235:genetics / Q000378:metabolism; D012097:Repressor Proteins / Q000378:metabolism; D064067:Rho Guanine Nucleotide Exchange Factors; D020825:T-Box Domain Proteins / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; D004268:DNA-Binding Proteins; D020662:Guanine Nucleotide Exchange Factors; D006657:Histones; C501641:MYH7 protein, human; D009124:Muscle Proteins; D000072041:PAX3 Transcription Factor; C489409:PAX3 protein, human; D051761:Paired Box Transcription Factors; D011518:Proto-Oncogene Proteins; D012097:Repressor Proteins; D064067:Rho Guanine Nucleotide Exchange Factors; D020825:T-Box Domain Proteins; C108625:TBX1 protein, human; C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D003596:Cytosine; D006899:Mixed Function Oxygenases; C462539:TET1 protein, human; D049308:Dioxygenases; C541081:TET2 protein, human; C578224:OBSCN protein, human; D017346:Protein Serine-Threonine Kinases; D024722:Cardiac Myosins; D018995:Myosin Heavy Chains
keywords: 5-hydroxymethylcytosine; DNA methylation; DNaseI hypersensitivity; TET1,; alternative splicing; enhancers; facioscapulohumeral muscular dystrophy; histone H3 methylation; muscle; myoblasts