Molecular Profiling of DNA Methylation and Alternative Splicing of Genes in Skeletal Muscle of Obese Rabbits
DNA methylation and the alternative splicing of precursor messenger RNAs (pre-mRNAs) are two important genetic modification mechanisms. However, both are currently uncharacterized in the muscle metabolism of rabbits. Thus, we constructed the Tianfu black rabbit obesity model (obese rabbits fed with...
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MDPI AG
2021-10-01
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| Series: | Current Issues in Molecular Biology |
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| Online Access: | https://www.mdpi.com/1467-3045/43/3/110 |
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| author | Yanhong Li Jie Wang Mauricio A. Elzo Huimei Fan Kun Du Siqi Xia Jiahao Shao Tianfu Lai Shenqiang Hu Xianbo Jia Songjia Lai |
| author_facet | Yanhong Li Jie Wang Mauricio A. Elzo Huimei Fan Kun Du Siqi Xia Jiahao Shao Tianfu Lai Shenqiang Hu Xianbo Jia Songjia Lai |
| author_sort | Yanhong Li |
| collection | DOAJ |
| description | DNA methylation and the alternative splicing of precursor messenger RNAs (pre-mRNAs) are two important genetic modification mechanisms. However, both are currently uncharacterized in the muscle metabolism of rabbits. Thus, we constructed the Tianfu black rabbit obesity model (obese rabbits fed with a 10% high-fat diet and control rabbits from 35 days to 70 days) and collected the skeletal muscle samples from the two groups for Genome methylation sequencing and RNA sequencing. DNA methylation data showed that the promoter regions of 599 genes and gene body region of 2522 genes had significantly differential methylation rates between the two groups, of which 288 genes had differential methylation rates in promoter and gene body regions. Analysis of alternative splicing showed 555 genes involved in exon skipping (ES) patterns, and 15 genes existed in differential methylation regions. Network analysis showed that 20 hub genes were associated with ubiquitinated protein degradation, muscle development pathways, and skeletal muscle energy metabolism. Our findings suggest that the two types of genetic modification have potential regulatory effects on skeletal muscle development and provide a basis for further mechanistic studies in the rabbit. |
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| issn | 1467-3037 1467-3045 |
| language | English |
| last_indexed | 2024-03-10T04:23:47Z |
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| series | Current Issues in Molecular Biology |
| spelling | doaj.art-4f63b9a3891b4553b4da2cc8932a78e82023-11-23T07:43:47ZengMDPI AGCurrent Issues in Molecular Biology1467-30371467-30452021-10-014331558157510.3390/cimb43030110Molecular Profiling of DNA Methylation and Alternative Splicing of Genes in Skeletal Muscle of Obese RabbitsYanhong Li0Jie Wang1Mauricio A. Elzo2Huimei Fan3Kun Du4Siqi Xia5Jiahao Shao6Tianfu Lai7Shenqiang Hu8Xianbo Jia9Songjia Lai10College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, ChinaCollege of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, ChinaDepartment of Animal Sciences, University of Florida, Gainesville, FL 32611, USACollege of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, ChinaCollege of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, ChinaCollege of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, ChinaCollege of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, ChinaCollege of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, ChinaCollege of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, ChinaCollege of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, ChinaCollege of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, ChinaDNA methylation and the alternative splicing of precursor messenger RNAs (pre-mRNAs) are two important genetic modification mechanisms. However, both are currently uncharacterized in the muscle metabolism of rabbits. Thus, we constructed the Tianfu black rabbit obesity model (obese rabbits fed with a 10% high-fat diet and control rabbits from 35 days to 70 days) and collected the skeletal muscle samples from the two groups for Genome methylation sequencing and RNA sequencing. DNA methylation data showed that the promoter regions of 599 genes and gene body region of 2522 genes had significantly differential methylation rates between the two groups, of which 288 genes had differential methylation rates in promoter and gene body regions. Analysis of alternative splicing showed 555 genes involved in exon skipping (ES) patterns, and 15 genes existed in differential methylation regions. Network analysis showed that 20 hub genes were associated with ubiquitinated protein degradation, muscle development pathways, and skeletal muscle energy metabolism. Our findings suggest that the two types of genetic modification have potential regulatory effects on skeletal muscle development and provide a basis for further mechanistic studies in the rabbit.https://www.mdpi.com/1467-3045/43/3/110DNA methylationalternative splicingmetabolic networkskeletal musclerabbit |
| spellingShingle | Yanhong Li Jie Wang Mauricio A. Elzo Huimei Fan Kun Du Siqi Xia Jiahao Shao Tianfu Lai Shenqiang Hu Xianbo Jia Songjia Lai Molecular Profiling of DNA Methylation and Alternative Splicing of Genes in Skeletal Muscle of Obese Rabbits Current Issues in Molecular Biology DNA methylation alternative splicing metabolic network skeletal muscle rabbit |
| title | Molecular Profiling of DNA Methylation and Alternative Splicing of Genes in Skeletal Muscle of Obese Rabbits |
| title_full | Molecular Profiling of DNA Methylation and Alternative Splicing of Genes in Skeletal Muscle of Obese Rabbits |
| title_fullStr | Molecular Profiling of DNA Methylation and Alternative Splicing of Genes in Skeletal Muscle of Obese Rabbits |
| title_full_unstemmed | Molecular Profiling of DNA Methylation and Alternative Splicing of Genes in Skeletal Muscle of Obese Rabbits |
| title_short | Molecular Profiling of DNA Methylation and Alternative Splicing of Genes in Skeletal Muscle of Obese Rabbits |
| title_sort | molecular profiling of dna methylation and alternative splicing of genes in skeletal muscle of obese rabbits |
| topic | DNA methylation alternative splicing metabolic network skeletal muscle rabbit |
| url | https://www.mdpi.com/1467-3045/43/3/110 |
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