Exploring the lncRNAs Related to Skeletal Muscle Fiber Types and Meat Quality Traits in Pigs

Abstract

The alteration in skeletal muscle fiber is a critical factor affecting livestock meat quality traits and human metabolic diseases. Long non-coding RNAs (lncRNAs) are a diverse class of non-coding RNAs with a length of more than 200 nucleotides. However, the mechanisms underlying the regulation of lncRNAs in skeletal muscle fibers remain elusive. To understand the genetic basis of lncRNA-regulated skeletal muscle fiber development, we performed a transcriptome analysis to identify the key lncRNAs affecting skeletal muscle fiber and meat quality traits on a pig model. We generated the lncRNA expression profiles of fast-twitch Biceps femoris (Bf) and slow-twitch Soleus (Sol) muscles and identified the differentially expressed (DE) lncRNAs using RNA-seq and performed bioinformatics analyses. This allowed us to identify 4581 lncRNA genes among six RNA libraries and 92 DE lncRNAs between Bf and Sol which are the key candidates for the conversion of skeletal muscle fiber types. Moreover, we detected the expression patterns of lncRNA MSTRG.42019 in different tissues and skeletal muscles of various development stages. In addition, we performed a correlation analyses between the expression of DE lncRNA MSTRG.42019 and meat quality traits. Notably, we found that DE lncRNA MSTRG.42019 was highly expressed in skeletal muscle and its expression was significantly higher in Sol than in Bf, with a positive correlation with the expression of Myosin heavy chain 7 (MYH7) (r = 0.6597, p = 0.0016) and a negative correlation with meat quality traits glycolytic potential (r = −0.5447, p = 0.0130), as well as drip loss (r = −0.5085, p = 0.0221). Moreover, we constructed the lncRNA MSTRG.42019–mRNAs regulatory network for a better understanding of a possible mechanism regulating skeletal muscle fiber formation. Our data provide the groundwork for studying the lncRNA regulatory mechanisms of skeletal muscle fiber conversion, and given the importance of skeletal muscle fiber types in muscle-related diseases, our data may provide insight into the treatment of muscular diseases in humans.

Integration of Long Non-Coding RNA and mRNA Profiling Reveals the Mechanisms of Different Dietary NFC/NDF Ratios Induced Rumen Development in Calves

“…In the current research, 47 differentially expressed lncRNAs, as well as 210 differentially expressed TUCPs and 1304 differentially expressed mRNAs were identified. The newly identified lncRNAs from rumen were shorter in length, fewer in exon number, lower in expression level and less conserved than protein-coding transcripts [ 28 ]. Integration of differentially expressed lncRNAs and DEGs found that 47 DE-lncRNAs regulated 860 DEGs.…”

An Analysis of Differentially Expressed Coding and Long Non-Coding RNAs in Multiple Models of Skeletal Muscle Atrophy

“…In addition, denervation and cancer cachexia increase the activity of satellite cells [ 49 , 50 ], and casting and fasting decrease the number of satellite cells [ 51 , 52 ]. Recently, Li et al found that the lncRNA MSTRG.42019 was associated with skeletal muscle fiber-type switching in pigs [ 53 ]. Several lncRNAs, such as LncMyoD , SAM , H19 , and CTTN-IT1 , affect the activity of satellite cells in mice, pigs, and sheep [ 54 , 55 , 56 , 57 ].…”

LncRNA-FKBP1C regulates muscle fiber type switching by affecting the stability of MYH1B

“…Skeletal muscle is one of the most dynamic tissues involved in a variety of biological processes 1 , and the growth and development of skeletal muscle are essential for maintaining skeletal muscle function 2 . Skeletal muscle dysfunction can lead to a variety of human muscle diseases, including muscle dystrophy, type 2 diabetes, cardiomyopathic disease, and other metabolic disorders 3 – 7 .…”

“…Previous research has reported that the ratio of muscle fiber types could affect meat quality 11 – 13 . In addition, skeletal muscle is dynamic muscle tissue, the fast muscle fiber subtype (type II) and the slow muscle fiber subtype (type I) can mutually transform regulated by noncoding RNAs 2 , 14 , 15 .…”