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Open Access Research article

Genome-wide DNA methylation changes in skeletal muscle between young and middle-aged pigs

Long Jin1, Zhi Jiang2, Yudong Xia3, Ping’er Lou1, Lei Chen4, Hongmei Wang1, Lu Bai1, Yanmei Xie1, Yihui Liu1, Wei Li1, Bangsheng Zhong1, Junfang Shen5, An’an Jiang1, Li Zhu1, Jinyong Wang4, Xuewei Li1* and Mingzhou Li1*

Author Affiliations

1 Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya’an, Sichuan 625014, China

2 Novogene Bioinformatics Institute, Beijing 100083, China

3 E-GENE, Shenzhen, Guangdong 518173, China

4 Chongqing Academy of Animal Science, Chongqing 402460, China

5 BGI-Tech, BGI-Shenzhen, Shenzhen 518083, China

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BMC Genomics 2014, 15:653  doi:10.1186/1471-2164-15-653

Published: 5 August 2014

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.

Keywords:
DNA methylation; Skeletal muscle; Pig; Aging; MeDIP-seq; DNMTs