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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #311578

Research Project: Understanding Genetic and Physiological Factors Affecting Nutrient Use Efficiency of Dairy Cattle

Location: Animal Genomics and Improvement Laboratory

Title: Genome-wide DNA methylation profiles and their replationship with mRNA and the microRNA transcriptome in bovine muscle tissue (Bos Taurine)

Author
item Huang, Young-zhen - Northwest Agricultural & Forestry University
item Sun, Jia-jie - Northwest Agricultural & Forestry University
item Zhang, Liang-zhi - Northwest Agricultural & Forestry University
item Li, Congjun
item Womark, James - Texas A&m University
item Li, Zhuan-jian - Northwest Agricultural & Forestry University
item Lan, Xian-yong - Northwest Agricultural & Forestry University
item Lei, Chu-zhao - Northwest Agricultural & Forestry University
item Zhao, Xin - Northwest Agricultural & Forestry University
item Chen, Hong - Northwest Agricultural & Forestry University

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/15/2014
Publication Date: 10/13/2014
Citation: Huang, Y., Sun, J., Zhang, L., Li, C., Womark, J.E., Li, Z., Lan, X., Lei, C., Zhao, X., Chen, H. 2014. Genome-wide DNA methylation profiles and their replationship with mRNA and the microRNA transcriptome in bovine muscle tissue (Bos Taurine). Scientific Reports. 4:6546. DOI: 10.1038/srep06546.

Interpretive Summary: DNA methylation is a key epigenetic modification in mammals and has essential and important roles in muscle development. This report provides a genome-wide landscape of DNA methylomes and their relationships to mRNA and miRNA for fetal and adult muscle in cattle. We found that the differentially methylated regions are highly related to muscle development by regulating expression repression of both known muscle-related genes and novel genes. This comprehensive map provides a solid basis for exploring epigenetic mechanisms of muscle growth and development. The work performed in this study will serve as a valuable resource for future functional validation, and could aid in searching for epigenetic biomarkers for muscle growth prediction and promoting further development of beef cattle as a model organism for muscle research in humans and other mammals.

Technical Abstract: DNA methylation is a key epigenetic modification in mammals, having essential and important roles in muscle development. We sample longissimus thoracis tissues from a well-known elite native breed of Chinese Qinchuan cattle living within comparable environments at fetal and adult stages, using methylated DNA immunoprecipitation sequencing (MeDIP-Seq), mRNA sequencing (mRNA-Seq) and small RNA sequencing (small RNA-Seq). microRNAs (miRNAs) are a class of small RNAs that post-transcriptionally regulate gene expression in animals and plants; small RNA-Seq enables the discovery and profiling of microRNAs. We generate and provide a genome-wide landscapes of DNA methylomes and their relationships to mRNA and miRNA for fetal and adult muscle studies. We found that the differentially methylated regions in promoters are highly associated with muscle development via expression repression of both known muscle-related genes and novel genes. Furthermore, we identified the expression patterns of the high-read negative correlation gene between expression level and DNA methylation modification on the promoter (upstream-2kb) level from nine differential tissues at multiple developmental stages of bovine muscle-related tissue or organs. Together, these results provide valuable data for future studies on biomedical research and genomic and epigenomic studies of cattle that may also help uncover the molecular basis that underlies economically valuable traits in cattle. The analysis shows global similarity and difference between fetal and adult stage and identifies the differentially methylated genes. This comprehensive map provides a solid basis for exploring epigenetic mechanisms of muscle growth and development.