Integrated Analysis of DNA Methylome and Transcriptome Reveals Regulatory Mechanism in the Longissimus Dorsi of Duroc Pigs
DNA methylation plays a pivotal role in the epigenetic regulation of gene expression and holds promise for enhancing livestock meat production. In this study, we analyzed the DNA methylome and transcriptome of the longissimus dorsi muscle (LDM) in Duroc pigs with varying growth rates. Our results re...
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2025-05-01
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| author | Shiyin Li Yarui Gao Lixia Ma Wei Chen Zhao Ma Zhanchi Ren Yunzhou Wang Yongqing Zeng |
| author_facet | Shiyin Li Yarui Gao Lixia Ma Wei Chen Zhao Ma Zhanchi Ren Yunzhou Wang Yongqing Zeng |
| author_sort | Shiyin Li |
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| description | DNA methylation plays a pivotal role in the epigenetic regulation of gene expression and holds promise for enhancing livestock meat production. In this study, we analyzed the DNA methylome and transcriptome of the longissimus dorsi muscle (LDM) in Duroc pigs with varying growth rates. Our results reveal that DNA methylation suppressed the expression of key muscle development markers (<i>MYOD</i>, <i>MYOG</i>, <i>MHC1</i>) and proliferation markers (<i>PI67</i>, <i>PCNA</i>), as well as the protein expression and phosphorylation of PI3K and AKT (<i>p</i> < 0.05). Dual-luciferase reporter assays and EMSA showed that SP1 overexpression enhanced the luciferase activity of the wild-type <i>LPAR1</i> promoter, an effect amplified by the demethylating agent 5-AZA (<i>p</i> < 0.05). The EMSA further demonstrates the relationship between SP1 and the <i>LPAR1</i> promoter region. Overexpression of SP1 upregulated <i>LPAR1</i> expression at both the mRNA and protein levels (<i>p</i> < 0.05). Knockdown of <i>LPAR1</i> reduced muscle marker gene expression and delayed myotube formation, while silencing <i>SP1</i> disrupted the expression of <i>LPAR1</i>, <i>MEF2C</i>, and <i>MHC1</i> (<i>p</i> < 0.05), and the demethylation induced by 5-AZA partially reversed these effects. These findings suggest that the DNA methylation/<i>SP1</i>/<i>LPAR1</i> axis is critical for skeletal muscle growth and development, underscoring the regulatory role of DNA methylation in muscle formation. |
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| institution | Kabale University |
| issn | 2073-4409 |
| language | English |
| publishDate | 2025-05-01 |
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| series | Cells |
| spelling | doaj-art-df74ff65d2374a64bbc3df02c02e2c4c2025-08-20T03:46:48ZengMDPI AGCells2073-44092025-05-01141178610.3390/cells14110786Integrated Analysis of DNA Methylome and Transcriptome Reveals Regulatory Mechanism in the Longissimus Dorsi of Duroc PigsShiyin Li0Yarui Gao1Lixia Ma2Wei Chen3Zhao Ma4Zhanchi Ren5Yunzhou Wang6Yongqing Zeng7Shandong Provincial Key Laboratory for Livestock Germplasm Innovation & Utilization, College of Animal Science and Technology, Shandong Agricultural University, Tai’an 271018, ChinaShandong Provincial Key Laboratory for Livestock Germplasm Innovation & Utilization, College of Animal Science and Technology, Shandong Agricultural University, Tai’an 271018, ChinaDepartment of Veterinary Medicine, Shandong Vocational Animal Science and Veterinary College, Weifang 261061, ChinaShandong Provincial Key Laboratory for Livestock Germplasm Innovation & Utilization, College of Animal Science and Technology, Shandong Agricultural University, Tai’an 271018, ChinaShandong Provincial Key Laboratory for Livestock Germplasm Innovation & Utilization, College of Animal Science and Technology, Shandong Agricultural University, Tai’an 271018, ChinaShandong Provincial Key Laboratory for Livestock Germplasm Innovation & Utilization, College of Animal Science and Technology, Shandong Agricultural University, Tai’an 271018, ChinaDepartment of Veterinary Medicine, Shandong Vocational Animal Science and Veterinary College, Weifang 261061, ChinaShandong Provincial Key Laboratory for Livestock Germplasm Innovation & Utilization, College of Animal Science and Technology, Shandong Agricultural University, Tai’an 271018, ChinaDNA methylation plays a pivotal role in the epigenetic regulation of gene expression and holds promise for enhancing livestock meat production. In this study, we analyzed the DNA methylome and transcriptome of the longissimus dorsi muscle (LDM) in Duroc pigs with varying growth rates. Our results reveal that DNA methylation suppressed the expression of key muscle development markers (<i>MYOD</i>, <i>MYOG</i>, <i>MHC1</i>) and proliferation markers (<i>PI67</i>, <i>PCNA</i>), as well as the protein expression and phosphorylation of PI3K and AKT (<i>p</i> < 0.05). Dual-luciferase reporter assays and EMSA showed that SP1 overexpression enhanced the luciferase activity of the wild-type <i>LPAR1</i> promoter, an effect amplified by the demethylating agent 5-AZA (<i>p</i> < 0.05). The EMSA further demonstrates the relationship between SP1 and the <i>LPAR1</i> promoter region. Overexpression of SP1 upregulated <i>LPAR1</i> expression at both the mRNA and protein levels (<i>p</i> < 0.05). Knockdown of <i>LPAR1</i> reduced muscle marker gene expression and delayed myotube formation, while silencing <i>SP1</i> disrupted the expression of <i>LPAR1</i>, <i>MEF2C</i>, and <i>MHC1</i> (<i>p</i> < 0.05), and the demethylation induced by 5-AZA partially reversed these effects. These findings suggest that the DNA methylation/<i>SP1</i>/<i>LPAR1</i> axis is critical for skeletal muscle growth and development, underscoring the regulatory role of DNA methylation in muscle formation.https://www.mdpi.com/2073-4409/14/11/786Duroc pigskeletal muscleWGBSDNA methylation<i>LPAR1</i> |
| spellingShingle | Shiyin Li Yarui Gao Lixia Ma Wei Chen Zhao Ma Zhanchi Ren Yunzhou Wang Yongqing Zeng Integrated Analysis of DNA Methylome and Transcriptome Reveals Regulatory Mechanism in the Longissimus Dorsi of Duroc Pigs Cells Duroc pig skeletal muscle WGBS DNA methylation <i>LPAR1</i> |
| title | Integrated Analysis of DNA Methylome and Transcriptome Reveals Regulatory Mechanism in the Longissimus Dorsi of Duroc Pigs |
| title_full | Integrated Analysis of DNA Methylome and Transcriptome Reveals Regulatory Mechanism in the Longissimus Dorsi of Duroc Pigs |
| title_fullStr | Integrated Analysis of DNA Methylome and Transcriptome Reveals Regulatory Mechanism in the Longissimus Dorsi of Duroc Pigs |
| title_full_unstemmed | Integrated Analysis of DNA Methylome and Transcriptome Reveals Regulatory Mechanism in the Longissimus Dorsi of Duroc Pigs |
| title_short | Integrated Analysis of DNA Methylome and Transcriptome Reveals Regulatory Mechanism in the Longissimus Dorsi of Duroc Pigs |
| title_sort | integrated analysis of dna methylome and transcriptome reveals regulatory mechanism in the longissimus dorsi of duroc pigs |
| topic | Duroc pig skeletal muscle WGBS DNA methylation <i>LPAR1</i> |
| url | https://www.mdpi.com/2073-4409/14/11/786 |
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