Construction of ceRNA networks of lncRNA and miRNA associated with intramuscular fat deposition in Ujumqin sheep
IntroductionThe molecular mechanisms underlying intramuscular fat (IMF) deposition are crucial for enhancing lamb meat quality. This process is regulated by a network of transcription factors. Exploring the role of non-coding RNAs, particularly lncRNAs and miRNAs, in IMF deposition can clarify its c...
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Frontiers Media S.A.
2025-03-01
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| Series: | Frontiers in Veterinary Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fvets.2025.1559727/full |
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| author | Mingxi Lan Qing Qin Yuchun Xie Yuchun Xie Chongyan Zhang Chongyan Zhang Chongyan Zhang Zhichen Liu Xiaolong Xu Jingwen Zhang Songsong Xu Ji Yang Haijun Zhang Suhe Alatan Zhixin Wang Zhixin Wang Zhixin Wang Zhihong Liu Zhihong Liu Zhihong Liu |
| author_facet | Mingxi Lan Qing Qin Yuchun Xie Yuchun Xie Chongyan Zhang Chongyan Zhang Chongyan Zhang Zhichen Liu Xiaolong Xu Jingwen Zhang Songsong Xu Ji Yang Haijun Zhang Suhe Alatan Zhixin Wang Zhixin Wang Zhixin Wang Zhihong Liu Zhihong Liu Zhihong Liu |
| author_sort | Mingxi Lan |
| collection | DOAJ |
| description | IntroductionThe molecular mechanisms underlying intramuscular fat (IMF) deposition are crucial for enhancing lamb meat quality. This process is regulated by a network of transcription factors. Exploring the role of non-coding RNAs, particularly lncRNAs and miRNAs, in IMF deposition can clarify its complex genetics and offer resources for breeding Inner Mongolian local breeds.MethodsWe evaluated carcass and lamb meat quality parameters using 60 six-month-old Ujumqin sheep with similar body weights. To investigate non-coding RNA’s role in IMF deposition, we identified differentially expressed genes and pathways between the longissimus dorsi and femoral biceps. Additionally, we analyzed these genes and the lncRNA-miRNA-mRNA co-regulatory network in high- and low-IMF femoral biceps groups.ResultsWe identified 11,529 mRNAs (747 differentially expressed), 9,874 lncRNAs (1,428 differentially expressed), and 761 miRNAs (12 differentially expressed). GO and KEGG enrichment analyses showed these genes are involved in lipid metabolism, fatty acid oxidation, and energy metabolism. We constructed a ceRNA network with 12 lncRNAs, 4 miRNAs, and 6 mRNAs. Notably, lncRNA MSTRG.13155.1 interacts with miR-1343-3p_R + 2, promoting IMF deposition by releasing HADHA gene expression. Dual-luciferase reporter assays confirmed MSTRG.13155.1 and HADHA as miR-1343-3p_R + 2 targets. RT-qPCR validated the expression trends of key mRNAs, miRNAs, and lncRNAs, consistent with sequencing results.DiscussionOur comprehensive analysis of differentially expressed genes and pathways in Ujumqin sheep’s longissimus dorsi and femoral biceps, along with high- and low-IMF groups, has revealed the complex genetics of IMF deposition. This offers valuable resources for Inner Mongolian local breed selection. The interaction between lncRNA MSTRG.13155.1 and miR-1343-3p_R + 2, and their regulation of HADHA expression, provides new insights into IMF deposition mechanisms. Future research can explore these mechanisms’ universality and specificity across different breeds and environments. |
| format | Article |
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| institution | Kabale University |
| issn | 2297-1769 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Veterinary Science |
| spelling | doaj-art-95a8f3dfbfae475bad50740902262bfb2025-08-20T03:39:43ZengFrontiers Media S.A.Frontiers in Veterinary Science2297-17692025-03-011210.3389/fvets.2025.15597271559727Construction of ceRNA networks of lncRNA and miRNA associated with intramuscular fat deposition in Ujumqin sheepMingxi Lan0Qing Qin1Yuchun Xie2Yuchun Xie3Chongyan Zhang4Chongyan Zhang5Chongyan Zhang6Zhichen Liu7Xiaolong Xu8Jingwen Zhang9Songsong Xu10Ji Yang11Haijun Zhang12Suhe Alatan13Zhixin Wang14Zhixin Wang15Zhixin Wang16Zhihong Liu17Zhihong Liu18Zhihong Liu19Animal Science Department, Inner Mongolia Agricultural University, Hohhot, ChinaAnimal Science Department, Inner Mongolia Agricultural University, Hohhot, ChinaAnimal Science Department, Inner Mongolia Agricultural University, Hohhot, ChinaCollege of Animal Science and Technology, Hebei Science and Technology Normal University, Qinhuangdao, Hebei, ChinaAnimal Science Department, Inner Mongolia Agricultural University, Hohhot, ChinaKey Laboratory of Sheep & Goat Genetics, Breeding and Reproduction in Inner Mongolia, Inner Mongolia Agricultural University, Hohhot, ChinaKey Laboratory of Sheep & Goat Genetics and Breeding of Ministry of Agriculture Inner Mongolia Agricultural University, Hohhot, ChinaAnimal Science Department, Inner Mongolia Agricultural University, Hohhot, ChinaAnimal Science Department, Inner Mongolia Agricultural University, Hohhot, ChinaAnimal Science Department, Inner Mongolia Agricultural University, Hohhot, ChinaCollege of Animal Science and Technology, China Agricultural University, Beijing, ChinaCollege of Animal Science and Technology, China Agricultural University, Beijing, ChinaErdos Agricultural and Animal Husbandry Science Research Institute, Ordos, ChinaEast Ujumqin Banner Hishig Animal Husbandry Development Co., Ltd., East Ujumqin Banner, ChinaAnimal Science Department, Inner Mongolia Agricultural University, Hohhot, ChinaKey Laboratory of Sheep & Goat Genetics, Breeding and Reproduction in Inner Mongolia, Inner Mongolia Agricultural University, Hohhot, ChinaKey Laboratory of Sheep & Goat Genetics and Breeding of Ministry of Agriculture Inner Mongolia Agricultural University, Hohhot, ChinaAnimal Science Department, Inner Mongolia Agricultural University, Hohhot, ChinaKey Laboratory of Sheep & Goat Genetics, Breeding and Reproduction in Inner Mongolia, Inner Mongolia Agricultural University, Hohhot, ChinaKey Laboratory of Sheep & Goat Genetics and Breeding of Ministry of Agriculture Inner Mongolia Agricultural University, Hohhot, ChinaIntroductionThe molecular mechanisms underlying intramuscular fat (IMF) deposition are crucial for enhancing lamb meat quality. This process is regulated by a network of transcription factors. Exploring the role of non-coding RNAs, particularly lncRNAs and miRNAs, in IMF deposition can clarify its complex genetics and offer resources for breeding Inner Mongolian local breeds.MethodsWe evaluated carcass and lamb meat quality parameters using 60 six-month-old Ujumqin sheep with similar body weights. To investigate non-coding RNA’s role in IMF deposition, we identified differentially expressed genes and pathways between the longissimus dorsi and femoral biceps. Additionally, we analyzed these genes and the lncRNA-miRNA-mRNA co-regulatory network in high- and low-IMF femoral biceps groups.ResultsWe identified 11,529 mRNAs (747 differentially expressed), 9,874 lncRNAs (1,428 differentially expressed), and 761 miRNAs (12 differentially expressed). GO and KEGG enrichment analyses showed these genes are involved in lipid metabolism, fatty acid oxidation, and energy metabolism. We constructed a ceRNA network with 12 lncRNAs, 4 miRNAs, and 6 mRNAs. Notably, lncRNA MSTRG.13155.1 interacts with miR-1343-3p_R + 2, promoting IMF deposition by releasing HADHA gene expression. Dual-luciferase reporter assays confirmed MSTRG.13155.1 and HADHA as miR-1343-3p_R + 2 targets. RT-qPCR validated the expression trends of key mRNAs, miRNAs, and lncRNAs, consistent with sequencing results.DiscussionOur comprehensive analysis of differentially expressed genes and pathways in Ujumqin sheep’s longissimus dorsi and femoral biceps, along with high- and low-IMF groups, has revealed the complex genetics of IMF deposition. This offers valuable resources for Inner Mongolian local breed selection. The interaction between lncRNA MSTRG.13155.1 and miR-1343-3p_R + 2, and their regulation of HADHA expression, provides new insights into IMF deposition mechanisms. Future research can explore these mechanisms’ universality and specificity across different breeds and environments.https://www.frontiersin.org/articles/10.3389/fvets.2025.1559727/fullsheepIMFlncRNAmiRNAceRNA network |
| spellingShingle | Mingxi Lan Qing Qin Yuchun Xie Yuchun Xie Chongyan Zhang Chongyan Zhang Chongyan Zhang Zhichen Liu Xiaolong Xu Jingwen Zhang Songsong Xu Ji Yang Haijun Zhang Suhe Alatan Zhixin Wang Zhixin Wang Zhixin Wang Zhihong Liu Zhihong Liu Zhihong Liu Construction of ceRNA networks of lncRNA and miRNA associated with intramuscular fat deposition in Ujumqin sheep Frontiers in Veterinary Science sheep IMF lncRNA miRNA ceRNA network |
| title | Construction of ceRNA networks of lncRNA and miRNA associated with intramuscular fat deposition in Ujumqin sheep |
| title_full | Construction of ceRNA networks of lncRNA and miRNA associated with intramuscular fat deposition in Ujumqin sheep |
| title_fullStr | Construction of ceRNA networks of lncRNA and miRNA associated with intramuscular fat deposition in Ujumqin sheep |
| title_full_unstemmed | Construction of ceRNA networks of lncRNA and miRNA associated with intramuscular fat deposition in Ujumqin sheep |
| title_short | Construction of ceRNA networks of lncRNA and miRNA associated with intramuscular fat deposition in Ujumqin sheep |
| title_sort | construction of cerna networks of lncrna and mirna associated with intramuscular fat deposition in ujumqin sheep |
| topic | sheep IMF lncRNA miRNA ceRNA network |
| url | https://www.frontiersin.org/articles/10.3389/fvets.2025.1559727/full |
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