title: Genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA transcriptomes in oxidative and glycolytic skeletal muscles.
abstract: The physiological, biochemical and functional differences between oxidative and glycolytic muscles play important roles in human metabolic health and in animal meat quality. To explore these differences, we determined the genome-wide landscape of DNA methylomes and their relationship with the mRNA and miRNA transcriptomes of the oxidative muscle psoas major (PMM) and the glycolytic muscle longissimus dorsi (LDM). We observed the hypo-methylation of sub-telomeric regions. A high mitochondrial content contributed to fast replicative senescence in PMM. The differentially methylated regions (DMRs) in promoters (478) and gene bodies (5,718) were mainly enriched in GTPase regulator activity and signaling cascade-mediated pathways. Integration analysis revealed that the methylation status within gene promoters (or gene bodies) and miRNA promoters was negatively correlated with mRNA and miRNA expression, respectively. Numerous genes were closely related to distinct phenotypic traits between LDM and PMM. For example, the hyper-methylation and down-regulation of HK-2 and PFKFB4 were related to decrease glycolytic potential in PMM. In addition, promoter hypo-methylation and the up-regulation of miR-378 silenced the expression of the target genes and promoted capillary biosynthesis in PMM. Together, these results improve understanding of muscle metabolism and development from genomic and epigenetic perspectives.
authors: College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
authors: Linyuan
authors: L
authors: Shen
authors: College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
authors: Jingjing
authors: J
authors: Du
authors: E-GENE, Shenzhen, Guangdong, China.
authors: Yudong
authors: Y
authors: Xia
authors: College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
authors: Zhendong
authors: Z
authors: Tan
authors: Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education &Key Laboratory of Swine Genetics, Huazhong Agricultural University, Wuhan, China.
authors: Yuhua
authors: Y
authors: Fu
authors: Department of Animal Husbandry and Veterinary Medicine, Chengdu Agricultural College, Chengdu, Sichuan, China.
authors: Qiong
authors: Q
authors: Yang
authors: College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
authors: Xuewei
authors: X
authors: Li
authors: College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
authors: Guoqing
authors: G
authors: Tang
authors: Department of Biology, College of Life and Science, Sichuan Agricultural University, Chengdu, Sichuan, China.
authors: Yanzhi
authors: Y
authors: Jiang
authors: Chongqing Academy of Animal Science, Rongchang, Chongqing, China.
authors: Jinyong
authors: J
authors: Wang
authors: College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
authors: Mingzhou
authors: M
authors: Li
authors: College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
authors: Shunhua
authors: S
authors: Zhang
authors: College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
authors: Li
authors: L
authors: Zhu
mesh_terms: D000818:Animals; D019175:DNA Methylation / Q000502:physiology*; D055106:Genome-Wide Association Study; D006019:Glycolysis / Q000502:physiology; D035683:MicroRNAs / Q000096:biosynthesis / Q000235:genetics; D018482:Muscle, Skeletal / Q000378:metabolism*; D010084:Oxidation-Reduction; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics; D013552:Swine; D059467:Transcriptome / Q000502:physiology*
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger