title: Identification of genes differentially expressed in myogenin knock-down bovine muscle satellite cells during differentiation through RNA sequencing analysis.
abstract: BACKGROUND
  The expression of myogenic regulatory factors (MRFs) consisting of MyoD, Myf5, myogenin (MyoG) and MRF4 characterizes various phases of skeletal muscle development including myoblast proliferation, cell-cycle exit, cell fusion and the maturation of myotubes to form myofibers. Although it is well known that the function of MyoG cannot be compensated for other MRFs, the molecular mechanism by which MyoG controls muscle cell differentiation is still unclear. Therefore, in this study, RNA-Seq technology was applied to profile changes in gene expression in response to MyoG knock-down (MyoGkd) in primary bovine muscle satellite cells (MSCs).
  
  
  RESULTS
  About 61-64% of the reads of over 42 million total reads were mapped to more than 13,000 genes in the reference bovine genome. RNA-Seq analysis identified 8,469 unique genes that were differentially expressed in MyoGkd. Among these genes, 230 were up-regulated and 224 were down-regulated by at least four-fold. DAVID Functional Annotation Cluster (FAC) and pathway analysis of all up- and down-regulated genes identified overrepresentation for cell cycle and division, DNA replication, mitosis, organelle lumen, nucleoplasm and cytosol, phosphate metabolic process, phosphoprotein phosphatase activity, cytoskeleton and cell morphogenesis, signifying the functional implication of these processes and pathways during skeletal muscle development. The RNA-Seq data was validated by real time RT-PCR analysis for eight out of ten genes as well as five marker genes investigated.
  
  
  CONCLUSIONS
  This study is the first RNA-Seq based gene expression analysis of MyoGkd undertaken in primary bovine MSCs. Computational analysis of the differentially expressed genes has identified the significance of genes such as SAP30-like (SAP30L), Protein lyl-1 (LYL1), various matrix metalloproteinases, and several glycogenes in myogenesis. The results of the present study widen our knowledge of the molecular basis of skeletal muscle development and reveal the vital regulatory role of MyoG in retaining muscle cell differentiation.
authors.affiliation: School of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea; Bovine Genome Resources Bank, Yeungnam University, Gyeongsan, Republic of Korea.
authors.forename: Eun Ju
authors.initials: EJ
authors.lastname: Lee
authors.affiliation: School of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea.
authors.forename: Adeel
authors.initials: A
authors.lastname: Malik
authors.affiliation: School of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea.
authors.forename: Smritee
authors.initials: S
authors.lastname: Pokharel
authors.affiliation: School of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea.
authors.forename: Sarafraz
authors.initials: S
authors.lastname: Ahmad
authors.affiliation: School of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea.
authors.forename: Bilal Ahmad
authors.initials: BA
authors.lastname: Mir
authors.affiliation: School of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea.
authors.forename: Kyung Hyun
authors.initials: KH
authors.lastname: Cho
authors.affiliation: School of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea.
authors.forename: Jihoe
authors.initials: J
authors.lastname: Kim
authors.affiliation: Biomedical Manufacturing Technology Center, Korea Institute of Industrial Technology, Yeongcheon-si, Republic of Korea.
authors.forename: Joon Chan
authors.initials: JC
authors.lastname: Kong
authors.affiliation: Biomedical Manufacturing Technology Center, Korea Institute of Industrial Technology, Yeongcheon-si, Republic of Korea.
authors.forename: Dong-Mok
authors.initials: DM
authors.lastname: Lee
authors.affiliation: Hanwoo Experiment Station, National Institute of Animal Science, RDA, Pyeongchang, Republic of Korea.
authors.forename: Ki Yong
authors.initials: KY
authors.lastname: Chung
authors.affiliation: Department of Biology, Kyung Hee University, Seoul, Republic of Korea.
authors.forename: Sang Hoon
authors.initials: SH
authors.lastname: Kim
authors.affiliation: School of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea; Bovine Genome Resources Bank, Yeungnam University, Gyeongsan, Republic of Korea.
authors.forename: Inho
authors.initials: I
authors.lastname: Choi
mesh_terms: D000818:Animals; D002417:Cattle; D002454:Cell Differentiation / Q000235:genetics / Q000502:physiology*; D002478:Cells, Cultured; D007150:Immunohistochemistry; D018008:Myogenin / Q000235:genetics / Q000378:metabolism*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D032496:Satellite Cells, Skeletal Muscle / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D018008:Myogenin