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Genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA transcriptomes in oxidative and glycolytic skeletal muscles
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 a...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4999948/ https://www.ncbi.nlm.nih.gov/pubmed/27561200 http://dx.doi.org/10.1038/srep32186 |
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author | Shen, Linyuan Du, Jingjing Xia, Yudong Tan, Zhendong Fu, Yuhua Yang, Qiong Li, Xuewei Tang, Guoqing Jiang, Yanzhi Wang, Jinyong Li, Mingzhou Zhang, Shunhua Zhu, Li |
author_facet | Shen, Linyuan Du, Jingjing Xia, Yudong Tan, Zhendong Fu, Yuhua Yang, Qiong Li, Xuewei Tang, Guoqing Jiang, Yanzhi Wang, Jinyong Li, Mingzhou Zhang, Shunhua Zhu, Li |
author_sort | Shen, Linyuan |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-4999948 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-49999482016-09-07 Genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA transcriptomes in oxidative and glycolytic skeletal muscles Shen, Linyuan Du, Jingjing Xia, Yudong Tan, Zhendong Fu, Yuhua Yang, Qiong Li, Xuewei Tang, Guoqing Jiang, Yanzhi Wang, Jinyong Li, Mingzhou Zhang, Shunhua Zhu, Li Sci Rep Article 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. Nature Publishing Group 2016-08-26 /pmc/articles/PMC4999948/ /pubmed/27561200 http://dx.doi.org/10.1038/srep32186 Text en Copyright © 2016, The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article Shen, Linyuan Du, Jingjing Xia, Yudong Tan, Zhendong Fu, Yuhua Yang, Qiong Li, Xuewei Tang, Guoqing Jiang, Yanzhi Wang, Jinyong Li, Mingzhou Zhang, Shunhua Zhu, Li Genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA transcriptomes in oxidative and glycolytic skeletal muscles |
title | Genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA transcriptomes in oxidative and glycolytic skeletal muscles |
title_full | Genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA transcriptomes in oxidative and glycolytic skeletal muscles |
title_fullStr | Genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA transcriptomes in oxidative and glycolytic skeletal muscles |
title_full_unstemmed | Genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA transcriptomes in oxidative and glycolytic skeletal muscles |
title_short | Genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA transcriptomes in oxidative and glycolytic skeletal muscles |
title_sort | genome-wide landscape of dna methylomes and their relationship with mrna and mirna transcriptomes in oxidative and glycolytic skeletal muscles |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4999948/ https://www.ncbi.nlm.nih.gov/pubmed/27561200 http://dx.doi.org/10.1038/srep32186 |
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