Profiling and Functional Analysis of Long Noncoding RNAs and mRNAs during Porcine Skeletal Muscle Development

Abstract

Gene transcripts or mRNAs and long noncoding RNAs (lncRNAs) are differentially expressed during porcine skeletal muscle development. However, only a few studies have been conducted on skeletal muscle transcriptome in pigs based on timepoints according to the growth curve for porcine. Here, we investigated gene expression in Qingyu pigs at three different growth stages: the inflection point with the maximum growth rate (MGI), the inflection point of the gradually increasing stage to the rapidly increasing stage (GRI), and the inflection point of the rapidly increasing stage to the slowly increasing stage (RSI). Subsequently, we explored gene expression profiles during muscle development at the MGI, GRI and RSI stages by Ribo-Zero RNA sequencing. Qingyu pigs reached the MGI, GRI and RSI stages at 156.40, 23.82 and 288.97 days of age with 51.73, 3.14 and 107.03 kg body weight, respectively. A total of 14,530 mRNAs and 11,970 lncRNAs were identified at the three stages, and 645, 323 differentially expressed genes (DEGs) and 696, 760 differentially expressed lncRNAs (DELs) were identified in the GRI vs. MGI, and RSI vs. MGI, comparisons. Functional enrichment analysis revealed that genes involved in immune system development and energy metabolism (mainly relate to amino acid, carbohydrate and lipid) were enriched at the GRI and MGI stages, respectively, whereas genes involved in lipid metabolism were enriched at the RSI stage. We further characterized G1430, an abundant lncRNA. The full-length sequence (316 nt) of lncRNA G1430 was determined by rapid amplification of cDNA ends (RACE). Subcellular distribution analysis by quantitative real-time PCR (qRT-PCR) revealed that G1430 is a cytoplasmic lncRNA. Binding site prediction and dual luciferase assay showed that lncRNA G1430 directly binds to microRNA 133a (miR-133a). Our findings provide the basis for further investigation of the regulatory mechanisms and molecular genetics of muscle development in pigs.

Transcriptome Analysis Reveals the Profile of Long Non-Coding RNAs during Myogenic Differentiation in Goats

“…As one of the most important members of the ncRNA family, lncRNA plays a vital role in regulating the transcriptional and post-transcriptional expression of genes in muscles [ 7 , 17 ]. In the past, numerous lncRNAs have been discovered in livestock, and these molecules are demonstrated to have a key role in the development of a variety of tissues [ 6 , 8 , 18 , 19 , 20 ]. However, there are few studies on lncRNA transcriptome in muscle cell development, since most studies are conducted at the tissue level.…”

“…The long non-coding RNAs (lncRNAs) are a class of non-coding RNAs (ncRNAs) with a length greater than 200 nucleotides. In recent years, increasing evidence indicates that lncRNAs play an essential role in the growth and development of skeletal muscle cells in animals, thereby regulating muscle activity [ 4 , 5 , 6 , 7 , 8 ]. For example, lncRNA lnc-mg plays a key role in promoting myogenesis by functioning as a competing endogenous RNA (ceRNA) for microRNA-125b, thus controlling the amount of insulin-like growth factor 2 (IGF-2) protein [ 9 ].…”

tsRNA Landscape and Potential Function Network in Subcutaneous and Visceral Pig Adipose Tissue

“…DKY-B20131403). No new experimental animals were slaughtered in this study, and all tissue samples were obtained from our previous study [ 31 ].…”

Cooked pork-derived exosome nanovesicles mediate metabolic disorder—microRNA could be the culprit

“…The library construction and sequencing of exosomal miRNA and liver mRNA was performed by Lianchuan BioTech Co., Ltd (Lianchuan Bio, Hangzhou, China). A previous methodology was adopted to perform the RNA-seq analyses [16,17]. Differentially expressed genes (DEGs) were identified using the edgeR software (|logFC|> 1, p value < 0.05).…”