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

BMC Genomics

Research Article

Junfang Shen¹  Jinyong Wang²  Lei Chen²  Yudong Xia³  Long Jin⁴  An’an Jiang⁴  Li Zhu⁴  Bangsheng Zhong⁴  Yihui Liu⁴  Xuewei Li⁴  Mingzhou Li⁴  Lu Bai⁴  Wei Li⁴  Ping’er Lou⁴  Hongmei Wang⁴  Yanmei Xie⁴  Zhi Jiang⁵ 

[1] BGI-Tech, BGI-Shenzhen, 518083, Shenzhen, China;Chongqing Academy of Animal Science, 402460, Chongqing, China;E-GENE, 518173, Shenzhen, Guangdong, China;Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, 625014, Ya’an, Sichuan, China;Novogene Bioinformatics Institute, 100083, Beijing, China;

关键词: DNA methylation;    Skeletal muscle;    Pig;    Aging;    MeDIP-seq;    DNMT;   

DOI  :  10.1186/1471-2164-15-653

 received in 2014-05-01, accepted in 2014-07-31,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundAge-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.ResultsWe 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.ConclusionsThis 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.

【 授权许可】

Unknown   
© Jin et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.