Hum Mol Genet. 2015 Jan 15;24(2):410-23. doi: 10.1093/hmg/ddu457. Epub 2014 Sep 4.

DNA methylation analysis of human myoblasts during in vitro myogenic differentiation: de novo methylation of promoters of muscle-related genes and its involvement in transcriptional down-regulation.

Miyata K¹, Miyata T², Nakabayashi K³, Okamura K⁴, Naito M⁵, Kawai T⁶, Takada S⁴, Kato K⁷, Miyamoto S⁸, Hata K⁶, Asahara H⁹.

Author information

1: Department of Systems BioMedicine and Department of Obstetrics and Gynecology, Faculty of Medicine, Fukuoka University, Fukuoka 814-0180, Japan.
2: Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.
3: Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan nakabaya-k@ncchd.go.jp asahara.syst@tmd.ac.jp.
4: Department of Systems BioMedicine and.
5: Department of Systems BioMedicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan and.
6: Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan.
7: Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.
8: Department of Obstetrics and Gynecology, Faculty of Medicine, Fukuoka University, Fukuoka 814-0180, Japan.
9: Department of Systems BioMedicine and Department of Systems BioMedicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan and Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA nakabaya-k@ncchd.go.jp asahara.syst@tmd.ac.jp.

Abstract

Although DNA methylation is considered to play an important role during myogenic differentiation, chronological alterations in DNA methylation and gene expression patterns in this process have been poorly understood. Using the Infinium HumanMethylation450 BeadChip array, we obtained a chronological profile of the genome-wide DNA methylation status in a human myoblast differentiation model, where myoblasts were cultured in low-serum medium to stimulate myogenic differentiation. As the differentiation of the myoblasts proceeded, their global DNA methylation level increased and their methylation patterns became more distinct from those of mesenchymal stem cells. Gene ontology analysis revealed that genes whose promoter region was hypermethylated upon myoblast differentiation were highly significantly enriched with muscle-related terms such as 'muscle contraction' and 'muscle system process'. Sequence motif analysis identified 8-bp motifs somewhat similar to the binding motifs of ID4 and ZNF238 to be most significantly enriched in hypermethylated promoter regions. ID4 and ZNF238 have been shown to be critical transcriptional regulators of muscle-related genes during myogenic differentiation. An integrated analysis of DNA methylation and gene expression profiles revealed that de novo DNA methylation of non-CpG island (CGI) promoters was more often associated with transcriptional down-regulation than that of CGI promoters. These results strongly suggest the existence of an epigenetic mechanism in which DNA methylation modulates the functions of key transcriptional factors to coordinately regulate muscle-related genes during myogenic differentiation.