title: Genome-wide DNA methylation profiles and their relationships with mRNA and the microRNA transcriptome in bovine muscle tissue (Bos taurine).
abstract: DNA methylation is a key epigenetic modification in mammals and plays important roles in muscle development. We sampled longissimus dorsi muscle (LDM) from a well-known elite native breed of Chinese Qinchuan cattle living within the same environment but displaying distinct skeletal muscle at the fetal and adult stages. We generated and provided a genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA for fetal and adult muscle studies. Integration analysis revealed a total of 77 and 1,054 negatively correlated genes with methylation in the promoter and gene body regions, respectively, in both the fetal and adult bovine libraries. Furthermore, we identified expression patterns of high-read genes that exhibit a negative correlation between methylation and expression from nine different tissues at multiple developmental stages of bovine muscle-related tissue or organs. In addition, we validated the MeDIP-Seq results by bisulfite sequencing PCR (BSP) in some of the differentially methylated promoters. Together, these results provide valuable data for future biomedical research and genomic and epigenomic studies of bovine skeletal muscle that may help uncover the molecular basis underlying economically valuable traits in cattle. This comprehensive map also provides a solid basis for exploring the epigenetic mechanisms of muscle growth and development.
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi, People's Republic of China.
authors.forename: Yong-Zhen
authors.initials: YZ
authors.lastname: Huang
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi, People's Republic of China.
authors.forename: Jia-Jie
authors.initials: JJ
authors.lastname: Sun
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi, People's Republic of China.
authors.forename: Liang-Zhi
authors.initials: LZ
authors.lastname: Zhang
authors.affiliation: United States Department of Agriculture-Agricultural Research Service, Bovine Functional Genomics Laboratory, Beltsville, Maryland, United States of America.
authors.forename: Cong-Jun
authors.initials: CJ
authors.lastname: Li
authors.affiliation: Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, United States of America.
authors.forename: James E
authors.initials: JE
authors.lastname: Womack
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi, People's Republic of China.
authors.forename: Zhuan-Jian
authors.initials: ZJ
authors.lastname: Li
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi, People's Republic of China.
authors.forename: Xian-Yong
authors.initials: XY
authors.lastname: Lan
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi, People's Republic of China.
authors.forename: Chu-Zhao
authors.initials: CZ
authors.lastname: Lei
authors.affiliation: Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou Jiangsu, People's Republic of China.
authors.forename: Chun-Lei
authors.initials: CL
authors.lastname: Zhang
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi, People's Republic of China.
authors.forename: Xin
authors.initials: X
authors.lastname: Zhao
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi, People's Republic of China.
authors.forename: Hong
authors.initials: H
authors.lastname: Chen
mesh_terms: D000818:Animals; D002417:Cattle; D018899:CpG Islands; D019175:DNA Methylation / Q000235:genetics*; D044127:Epigenesis, Genetic; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000096:biosynthesis* / Q000235:genetics; D024510:Muscle Development / Q000235:genetics; D018482:Muscle, Skeletal / Q000254:growth & development / Q000378:metabolism; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger / Q000096:biosynthesis* / Q000235:genetics; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger