Construction of ceRNA networks of lncRNA and miRNA associated with intramuscular fat deposition in Ujumqin sheep

Mingxi Lan ¹ Qing Qin ¹ Yuchun Xie ² Chongyan Zhang ¹ Zhichen Liu ¹ Xiaolong Xu ¹ Jingwen Zhang ¹ Songsong Xu ³ Ji Yang ³ Haijun Zhang ⁴ Suhe Alatan ⁵ Zhixin Wang ¹ Zhihong Liu ^1*

• ¹ Inner Mongolia Agricultural University, Hohhot, China
• ² College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei Province, China
• ³ China Agricultural University, Beijing, Beijing Municipality, China
• ⁴ Erdos Agricultural and Animal Husbandry Technology Extension Center, Ordos, China
• ⁵ Ujumqin Banner Hishig Animal Husbandry Development Co., Ltd., Inner Mongolia Autonomous Region, China

The molecular mechanisms underlying intramuscular fat (IMF) deposition are pivotal in enhancing the quality of lamb meat. This process is intricately regulated by a network of multiple transcription factors. In our study, we utilized 60 Ujumqin sheep, all six months old and of comparable body weights, to evaluate carcass indices and lamb quality parameters. To delve deeper into the role of non-coding RNAs, particularly long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), in the molecular mechanisms of IMF deposition in Ujumqin sheep, we systematically identified differentially expressed genes and pathways between the longest dorsal muscle and the biceps femoris muscle. Furthermore, we conducted a comprehensive analysis of differentially expressed genes in high and low IMF groups of the biceps femoris muscle, as well as the lncRNA-miRNA-mRNA co-regulatory network. This comprehensive approach aims to elucidate the complex genetic architecture associated with IMF in Ujumqin sheep and to provide valuable resources and a theoretical foundation for the selection and breeding of local fine breeds in Inner Mongolia. Our study identified 11,529 mRNAs, of which 747 were differentially expressed; 9,874 lncRNAs, with 1,428 differentially expressed; and 761 miRNAs, of which 12 were differentially expressed. GO and KEGG enrichment analyses indicated that these differentially expressed genes are involved in key biological processes such as lipid metabolism, fatty acid oxidation, and energy metabolism. Notably, we constructed a competing endogenous RNA (ceRNA) network that includes 12 lncRNAs, 4 miRNAs, and 6 mRNAs. A significant finding was that lncRNA MSTRG.13155.1 interacts with miR-1343-3p_R+2, thereby releasing the expression of the HADHA gene and promoting IMF deposition. Dual luciferase reporter gene assays confirmed that MSTRG.13155.1 and HADHA are targets of miR-1343-3p_R+2. RT-qPCR validated the expression trends of key mRNAs, miRNAs, and lncRNAs, which were consistent with the sequencing results.