Alternative Splicing Novel lncRNAs and Their Target Genes in Ovine Skeletal Muscles

Long non-coding RNAs (lncRNAs) compose a plentiful category of transcripts that have gained increasing importance because of their roles in different biological processes. Although the function of most lncRNAs remains unclear. They are implicated in epigenetic regulation of gene expression, including muscle development and differentiation. We aimed to identify the effect of novel lncRNAs (Alternatively spliced) and their target genes on two stages of sheep skeletal muscle growth and development. FastQC files have been used to examine the quality control and the Trimmomatic program for trimming low-quality reads from twelve longissimus dorsal muscle tissue samples (including six young and six old from Texel sheep). Hisat۲, Cufflink, Cuffmerge, and Cuffdiff investigated the expression levels. Novel lncRNAs (Alternative spliced) were distinguished using NONCODE databases and Cuffcompare software. In addition, the lncRNA–mRNA interactions and regulatory network visualization were identified via RIsearch and Cytoscape software, respectively. Those ۱۳۹ novel lncRNA (Alternative spliced) transcripts had been recognized, probably ۶۵ lncRNAs interacted with their target genes and regulated sheep skeletal muscle growth and development. Three novel lncRNA transcripts (TCONS_۰۰۰۴۱۳۸۶, TCONS_۰۰۰۵۰۰۵۹, and TCONS_۰۰۰۵۶۴۲۸) showed a strong association and five transcripts (TCONS_۰۰۰۵۵۷۶۱, TCONS_۰۰۰۵۵۷۶۲, TCONS_۰۰۰۵۵۷۶۳, TCONS_۰۰۰۵۵۷۶۴, and TCONS_۰۰۰۵۵۷۷۰) had made complex network correlations with mRNAs. Our research provided more knowledge of the associated mechanisms with novel lncRNAs, which could play a role in regulating sheep skeletal muscle tissue development and growth.

Keywords:

Regulatory network , Novel lncRNAs , Skeletal muscle , Alternative splicing , Gene expression