Identification of Candidate Genes and Regulatory Competitive Endogenous RNA (ceRNA) Networks Underlying Intramuscular Fat Content in Yorkshire Pigs with Extreme Fat Deposition Phenotypes
Intramuscular fat (IMF) content is vital for pork quality, serving an important role in economic performance in pig industry. Non-coding RNAs, with mRNAs, are involved in IMF deposition; however, their functions and regulatory mechanisms in porcine IMF remain elusive. This study assessed the whole t...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-10-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/20/12596 |
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| author | Yueyun Ding Yinhui Hou Zijing Ling Qiong Chen Tao Xu Lifei Liu Na Yu Wenliang Ni Xiaoling Ding Xiaodong Zhang Xianrui Zheng Wenbin Bao Zongjun Yin |
| author_facet | Yueyun Ding Yinhui Hou Zijing Ling Qiong Chen Tao Xu Lifei Liu Na Yu Wenliang Ni Xiaoling Ding Xiaodong Zhang Xianrui Zheng Wenbin Bao Zongjun Yin |
| author_sort | Yueyun Ding |
| collection | DOAJ |
| description | Intramuscular fat (IMF) content is vital for pork quality, serving an important role in economic performance in pig industry. Non-coding RNAs, with mRNAs, are involved in IMF deposition; however, their functions and regulatory mechanisms in porcine IMF remain elusive. This study assessed the whole transcriptome expression profiles of the <i>Longissimus dorsi</i> muscle of pigs with high (H) and low (L) IMF content to identify genes implicated in porcine IMF adipogenesis and their regulatory functions. Hundreds of differentially expressed RNAs were found to be involved in fatty acid metabolic processes, lipid metabolism, and fat cell differentiation. Furthermore, combing co-differential expression analyses, we constructed competing endogenous RNAs (ceRNA) regulatory networks, showing crosstalk among 30 lncRNAs and 61 mRNAs through 20 miRNAs, five circRNAs and 11 mRNAs through four miRNAs, and potential IMF deposition-related ceRNA subnetworks. Functional lncRNAs and circRNAs (such as MSTRG.12440.1, ENSSSCT00000066779, novel_circ_011355, novel_circ_011355) were found to act as ceRNAs of important lipid metabolism-related mRNAs (<i>LEP</i>, <i>IP6K1</i>, <i>FFAR4</i>, <i>CEBPA</i>, etc.) by sponging functional miRNAs (such as ssc-miR-196a, ssc-miR-200b, ssc-miR10391, miR486-y). These findings provide potential regulators and molecular regulatory networks that can be utilized for research on IMF traits in pigs, which would aid in marker-assisted selection to improve pork quality. |
| first_indexed | 2024-03-09T12:14:33Z |
| format | Article |
| id | doaj.art-1d62a6360e154316ba3e7f2875a017ff |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T12:14:33Z |
| publishDate | 2022-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-1d62a6360e154316ba3e7f2875a017ff2023-11-30T22:48:00ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-10-0123201259610.3390/ijms232012596Identification of Candidate Genes and Regulatory Competitive Endogenous RNA (ceRNA) Networks Underlying Intramuscular Fat Content in Yorkshire Pigs with Extreme Fat Deposition PhenotypesYueyun Ding0Yinhui Hou1Zijing Ling2Qiong Chen3Tao Xu4Lifei Liu5Na Yu6Wenliang Ni7Xiaoling Ding8Xiaodong Zhang9Xianrui Zheng10Wenbin Bao11Zongjun Yin12College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, ChinaCollege of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, ChinaCollege of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, ChinaCollege of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, ChinaCollege of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, ChinaCollege of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, ChinaCollege of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, ChinaCollege of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, ChinaCollege of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, ChinaCollege of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, ChinaCollege of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, ChinaKey Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaCollege of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, ChinaIntramuscular fat (IMF) content is vital for pork quality, serving an important role in economic performance in pig industry. Non-coding RNAs, with mRNAs, are involved in IMF deposition; however, their functions and regulatory mechanisms in porcine IMF remain elusive. This study assessed the whole transcriptome expression profiles of the <i>Longissimus dorsi</i> muscle of pigs with high (H) and low (L) IMF content to identify genes implicated in porcine IMF adipogenesis and their regulatory functions. Hundreds of differentially expressed RNAs were found to be involved in fatty acid metabolic processes, lipid metabolism, and fat cell differentiation. Furthermore, combing co-differential expression analyses, we constructed competing endogenous RNAs (ceRNA) regulatory networks, showing crosstalk among 30 lncRNAs and 61 mRNAs through 20 miRNAs, five circRNAs and 11 mRNAs through four miRNAs, and potential IMF deposition-related ceRNA subnetworks. Functional lncRNAs and circRNAs (such as MSTRG.12440.1, ENSSSCT00000066779, novel_circ_011355, novel_circ_011355) were found to act as ceRNAs of important lipid metabolism-related mRNAs (<i>LEP</i>, <i>IP6K1</i>, <i>FFAR4</i>, <i>CEBPA</i>, etc.) by sponging functional miRNAs (such as ssc-miR-196a, ssc-miR-200b, ssc-miR10391, miR486-y). These findings provide potential regulators and molecular regulatory networks that can be utilized for research on IMF traits in pigs, which would aid in marker-assisted selection to improve pork quality.https://www.mdpi.com/1422-0067/23/20/12596non-coding RNAsceRNA networkIMFpigRNA-seq |
| spellingShingle | Yueyun Ding Yinhui Hou Zijing Ling Qiong Chen Tao Xu Lifei Liu Na Yu Wenliang Ni Xiaoling Ding Xiaodong Zhang Xianrui Zheng Wenbin Bao Zongjun Yin Identification of Candidate Genes and Regulatory Competitive Endogenous RNA (ceRNA) Networks Underlying Intramuscular Fat Content in Yorkshire Pigs with Extreme Fat Deposition Phenotypes International Journal of Molecular Sciences non-coding RNAs ceRNA network IMF pig RNA-seq |
| title | Identification of Candidate Genes and Regulatory Competitive Endogenous RNA (ceRNA) Networks Underlying Intramuscular Fat Content in Yorkshire Pigs with Extreme Fat Deposition Phenotypes |
| title_full | Identification of Candidate Genes and Regulatory Competitive Endogenous RNA (ceRNA) Networks Underlying Intramuscular Fat Content in Yorkshire Pigs with Extreme Fat Deposition Phenotypes |
| title_fullStr | Identification of Candidate Genes and Regulatory Competitive Endogenous RNA (ceRNA) Networks Underlying Intramuscular Fat Content in Yorkshire Pigs with Extreme Fat Deposition Phenotypes |
| title_full_unstemmed | Identification of Candidate Genes and Regulatory Competitive Endogenous RNA (ceRNA) Networks Underlying Intramuscular Fat Content in Yorkshire Pigs with Extreme Fat Deposition Phenotypes |
| title_short | Identification of Candidate Genes and Regulatory Competitive Endogenous RNA (ceRNA) Networks Underlying Intramuscular Fat Content in Yorkshire Pigs with Extreme Fat Deposition Phenotypes |
| title_sort | identification of candidate genes and regulatory competitive endogenous rna cerna networks underlying intramuscular fat content in yorkshire pigs with extreme fat deposition phenotypes |
| topic | non-coding RNAs ceRNA network IMF pig RNA-seq |
| url | https://www.mdpi.com/1422-0067/23/20/12596 |
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