1. Early de novo DNA methylation and prolonged demethylation in the muscle lineage.
- Author
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Tsumagari K, Baribault C, Terragni J, Varley KE, Gertz J, Pradhan S, Badoo M, Crain CM, Song L, Crawford GE, Myers RM, Lacey M, and Ehrlich M
- Subjects
- 5-Methylcytosine analogs & derivatives, Adolescent, Adult, Aged, Aged, 80 and over, CCCTC-Binding Factor, Cardiac Myosins genetics, Cardiac Myosins metabolism, Case-Control Studies, Child, Cytosine analogs & derivatives, Cytosine metabolism, DNA-Binding Proteins genetics, DNA-Binding Proteins metabolism, Dioxygenases, Epigenesis, Genetic, Female, Gene Expression Regulation, Developmental, Genes, Homeobox, Genome, Human, Guanine Nucleotide Exchange Factors genetics, Guanine Nucleotide Exchange Factors metabolism, Histones metabolism, Humans, Infant, Newborn, Male, Middle Aged, Mixed Function Oxygenases, Muscle Fibers, Skeletal metabolism, Muscle Proteins genetics, Muscle Proteins metabolism, Muscular Dystrophy, Facioscapulohumeral metabolism, Myoblasts metabolism, Myosin Heavy Chains genetics, Myosin Heavy Chains metabolism, PAX3 Transcription Factor, Paired Box Transcription Factors genetics, Paired Box Transcription Factors metabolism, Protein Serine-Threonine Kinases, Proto-Oncogene Proteins genetics, Proto-Oncogene Proteins metabolism, Repressor Proteins metabolism, Rho Guanine Nucleotide Exchange Factors, T-Box Domain Proteins genetics, T-Box Domain Proteins metabolism, Transcription, Genetic, Cell Lineage genetics, DNA Methylation, Muscle Development genetics, Muscular Dystrophy, Facioscapulohumeral genetics
- 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.
- Published
- 2013
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