Long-stranded non-coding RNAs temporal-specific expression profiles reveal longissimus dorsi muscle development and intramuscular fat deposition in Tianzhu white yak

Abstract

The process of muscle development and intramuscular fat (IMF) deposition is quite complex and controlled by both mRNAs and ncRNAs. Long-stranded non-coding RNAs (LncRNAs) are involved in various biological processes in mammals while also playing a critical role in muscle development and fat deposition. In the present study, RNA-Seq was used to comprehensively study the expression of lncRNAs and mRNAs during muscle development and intramuscular fat deposition in postnatal Tianzhu white yaks at three stages, including 6 months of age (calve, n=6), 30 months of age (young cattle, n=6) and 54 months of age (adult cattle, n=6). The results indicated that a total of 2101 lncRNAs and 20855 mRNAs were screened across the three stages, of which the numbers of differential expression (DE) lncRNAs and DE mRNAs were 289 and 1339, respectively, and DE lncRNAs were divided into eight different expression patterns based on expression trends. GO and KEGG enrichment analysis revealed that some DE mRNAs overlapped with target genes of lncRNAs, such as NEDD4L, SCN3B, AGT, HDAC4, DES, MYH14, KLF15 (muscle development), ACACB, PCK2, LIPE, PIK3R1, PNPLA2, MGLL (intramuscular fat deposition). These DE mRNAs were significantly enriched in critical muscle development and IMF deposition related pathways and GO terms, such as AMPK signaling pathway, PI3K-Akt signaling pathway, PPAR signaling pathway, etc. In addition, lncRNA-mRNA co-expression network analysis revealed that six lncRNAs (MSTRG.20152.2, MSTRG.20152.3, XR_001351700.1, MSTRG.8190.1, MSTRG.4827.1 and MSTRG.11486.1) may play a major role in Tianzhu white yak muscle development and lipidosis deposition. Therefore, this study enriches the database of yak lncRNAs and could help to further explore the functions and roles of lncRNAs in different stages of muscle development and intramuscular fat deposition in the Tianzhu white yak.