title: Genome-wide DNA methylation changes in skeletal muscle between young and middle-aged pigs.
abstract: BACKGROUND
  Age-related physiological, biochemical and functional changes in mammalian skeletal muscle have been shown to begin at the mid-point of the lifespan. However, the underlying changes in DNA methylation that occur during this turning point of the muscle aging process have not been clarified. To explore age-related genomic methylation changes in skeletal muscle, we employed young (0.5 years old) and middle-aged (7 years old) pigs as models to survey genome-wide DNA methylation in the longissimus dorsi muscle using a methylated DNA immunoprecipitation sequencing approach.
  
  
  RESULTS
  We observed a tendency toward a global loss of DNA methylation in the gene-body region of the skeletal muscle of the middle-aged pigs compared with the young group. We determined the genome-wide gene expression pattern in the longissimus dorsi muscle using microarray analysis and performed a correlation analysis using DMR (differentially methylated region)-mRNA pairs, and we found a significant negative correlation between the changes in methylation levels within gene bodies and gene expression. Furthermore, we identified numerous genes that show age-related methylation changes that are potentially involved in the aging process. The methylation status of these genes was confirmed using bisulfite sequencing PCR. The genes that exhibited a hypomethylated gene body in middle-aged pigs were over-represented in various proteolysis and protein catabolic processes, suggesting an important role for these genes in age-related muscle atrophy. In addition, genes associated with tumorigenesis exhibited aged-related differences in methylation and expression levels, suggesting an increased risk of disease associated with increased age.
  
  
  CONCLUSIONS
  This study provides a comprehensive analysis of genome-wide DNA methylation patterns in aging pig skeletal muscle. Our findings will serve as a valuable resource in aging studies, promoting the pig as a model organism for human aging research and accelerating the development of comparative animal models in aging research.
authors.forename: Long
authors.initials: L
authors.lastname: Jin
authors.forename: Zhi
authors.initials: Z
authors.lastname: Jiang
authors.forename: Yudong
authors.initials: Y
authors.lastname: Xia
authors.forename: Ping'er
authors.initials: P
authors.lastname: Lou
authors.forename: Lei
authors.initials: L
authors.lastname: Chen
authors.forename: Hongmei
authors.initials: H
authors.lastname: Wang
authors.forename: Lu
authors.initials: L
authors.lastname: Bai
authors.forename: Yanmei
authors.initials: Y
authors.lastname: Xie
authors.forename: Yihui
authors.initials: Y
authors.lastname: Liu
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.forename: Bangsheng
authors.initials: B
authors.lastname: Zhong
authors.forename: Junfang
authors.initials: J
authors.lastname: Shen
authors.forename: An'an
authors.initials: A
authors.lastname: Jiang
authors.forename: Li
authors.initials: L
authors.lastname: Zhu
authors.forename: Jinyong
authors.initials: J
authors.lastname: Wang
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan 625014, China. xuewei.li@sicau.edu.cn.
authors.forename: Xuewei
authors.initials: X
authors.lastname: Li
authors.forename: Mingzhou
authors.initials: M
authors.lastname: Li
mesh_terms: D000375:Aging; D000818:Animals; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005260:Female; D015870:Gene Expression; D016678:Genome; D018482:Muscle, Skeletal / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA; D034421:Sus scrofa / Q000502:physiology*; D016615:Telomere / Q000235:genetics
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