Cargando…
Genome-wide DNA methylation changes in skeletal muscle between young and middle-aged pigs
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 clarifie...
Autores principales: | , , , , , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4147169/ https://www.ncbi.nlm.nih.gov/pubmed/25096499 http://dx.doi.org/10.1186/1471-2164-15-653 |
_version_ | 1782332389787172864 |
---|---|
author | Jin, Long Jiang, Zhi Xia, Yudong Lou, Ping’er Chen, Lei Wang, Hongmei Bai, Lu Xie, Yanmei Liu, Yihui Li, Wei Zhong, Bangsheng Shen, Junfang Jiang, An’an Zhu, Li Wang, Jinyong Li, Xuewei Li, Mingzhou |
author_facet | Jin, Long Jiang, Zhi Xia, Yudong Lou, Ping’er Chen, Lei Wang, Hongmei Bai, Lu Xie, Yanmei Liu, Yihui Li, Wei Zhong, Bangsheng Shen, Junfang Jiang, An’an Zhu, Li Wang, Jinyong Li, Xuewei Li, Mingzhou |
author_sort | Jin, Long |
collection | PubMed |
description | 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-653) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4147169 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-41471692014-09-02 Genome-wide DNA methylation changes in skeletal muscle between young and middle-aged pigs Jin, Long Jiang, Zhi Xia, Yudong Lou, Ping’er Chen, Lei Wang, Hongmei Bai, Lu Xie, Yanmei Liu, Yihui Li, Wei Zhong, Bangsheng Shen, Junfang Jiang, An’an Zhu, Li Wang, Jinyong Li, Xuewei Li, Mingzhou BMC Genomics Research Article 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-653) contains supplementary material, which is available to authorized users. BioMed Central 2014-08-05 /pmc/articles/PMC4147169/ /pubmed/25096499 http://dx.doi.org/10.1186/1471-2164-15-653 Text en © 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. |
spellingShingle | Research Article Jin, Long Jiang, Zhi Xia, Yudong Lou, Ping’er Chen, Lei Wang, Hongmei Bai, Lu Xie, Yanmei Liu, Yihui Li, Wei Zhong, Bangsheng Shen, Junfang Jiang, An’an Zhu, Li Wang, Jinyong Li, Xuewei Li, Mingzhou Genome-wide DNA methylation changes in skeletal muscle between young and middle-aged pigs |
title | Genome-wide DNA methylation changes in skeletal muscle between young and middle-aged pigs |
title_full | Genome-wide DNA methylation changes in skeletal muscle between young and middle-aged pigs |
title_fullStr | Genome-wide DNA methylation changes in skeletal muscle between young and middle-aged pigs |
title_full_unstemmed | Genome-wide DNA methylation changes in skeletal muscle between young and middle-aged pigs |
title_short | Genome-wide DNA methylation changes in skeletal muscle between young and middle-aged pigs |
title_sort | genome-wide dna methylation changes in skeletal muscle between young and middle-aged pigs |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4147169/ https://www.ncbi.nlm.nih.gov/pubmed/25096499 http://dx.doi.org/10.1186/1471-2164-15-653 |
work_keys_str_mv | AT jinlong genomewidednamethylationchangesinskeletalmusclebetweenyoungandmiddleagedpigs AT jiangzhi genomewidednamethylationchangesinskeletalmusclebetweenyoungandmiddleagedpigs AT xiayudong genomewidednamethylationchangesinskeletalmusclebetweenyoungandmiddleagedpigs AT loupinger genomewidednamethylationchangesinskeletalmusclebetweenyoungandmiddleagedpigs AT chenlei genomewidednamethylationchangesinskeletalmusclebetweenyoungandmiddleagedpigs AT wanghongmei genomewidednamethylationchangesinskeletalmusclebetweenyoungandmiddleagedpigs AT bailu genomewidednamethylationchangesinskeletalmusclebetweenyoungandmiddleagedpigs AT xieyanmei genomewidednamethylationchangesinskeletalmusclebetweenyoungandmiddleagedpigs AT liuyihui genomewidednamethylationchangesinskeletalmusclebetweenyoungandmiddleagedpigs AT liwei genomewidednamethylationchangesinskeletalmusclebetweenyoungandmiddleagedpigs AT zhongbangsheng genomewidednamethylationchangesinskeletalmusclebetweenyoungandmiddleagedpigs AT shenjunfang genomewidednamethylationchangesinskeletalmusclebetweenyoungandmiddleagedpigs AT jianganan genomewidednamethylationchangesinskeletalmusclebetweenyoungandmiddleagedpigs AT zhuli genomewidednamethylationchangesinskeletalmusclebetweenyoungandmiddleagedpigs AT wangjinyong genomewidednamethylationchangesinskeletalmusclebetweenyoungandmiddleagedpigs AT lixuewei genomewidednamethylationchangesinskeletalmusclebetweenyoungandmiddleagedpigs AT limingzhou genomewidednamethylationchangesinskeletalmusclebetweenyoungandmiddleagedpigs |