Comprehensive Analysis of lncRNAs and circRNAs Reveals the Metabolic Specialization in Oxidative and Glycolytic Skeletal Muscles

Abstract

The biochemical and functional differences between oxidative and glycolytic muscles could affect human muscle health and animal meat quality. However, present understanding of the epigenetic regulation with respect to lncRNAs and circRNAs is rudimentary. Here, porcine oxidative and glycolytic skeletal muscles, which were at the growth curve inflection point, were sampled to survey variant global expression of lncRNAs and circRNAs using RNA-seq. A total of 4046 lncRNAs were identified, including 911 differentially expressed lncRNAs (p < 0.05). The cis-regulatory analysis identified target genes that were enriched for specific GO terms and pathways (p < 0.05), including the oxidation-reduction process, glycolytic process, and fatty acid metabolic. All these were closely related to different phenotypes between oxidative and glycolytic muscles. Additionally, 810 circRNAs were identified, of which 137 were differentially expressed (p < 0.05). Interestingly, some circRNA-miRNA-mRNA networks were found, which were closely linked to muscle fiber-type switching and mitochondria biogenesis in muscles. Furthermore, 44.69%, 39.19%, and 54.01% of differentially expressed mRNAs, lncRNAs, and circRNAs respectively were significantly enriched in pig quantitative trait loci (QTL) regions for growth and meat quality traits. This study reveals a mass of candidate lncRNAs and circRNAs involved in muscle physiological functions, which may improve understanding of muscle metabolism and development from an epigenetic perspective.

Circular RNA screening identifies circMYLK4 as a regulator of fast/slow myofibers in porcine skeletal muscles

“…Their study revealed a new post-transcriptional regulatory layer that could promote the understanding of the molecular mechanisms of muscle ber development in different breeds of pigs. Shen studied the circRNA expression pro les of the psoas major muscle and the longissimus dorsi muscle of 178-day-old Qingyu pigs and identi ed 810 circRNAs, of which 137 were differentially expressed [24]. These circRNAs may be involved in the regulatory network of muscle ber type.…”

Comprehensive analysis of circular RNA profiles in skeletal muscles of aging mice and after aerobic exercise intervention

“…Kotb et al identified and annotated many circRNAs in the skeletal muscles of Rhesus monkey via RNA-seq and verified the downregulation of mmu_circ_017332, mmu_ circ_014269, mmu_circ_015060, mmu_circ_006895, and mmu_circ_014509 during aging in monkeys [35]. In addition, previous reports have identified circFUT10, circLM07, circSVIL, circRBFOXO2, circFGFR2, circZFP609, circFGFR4 and circSNX29 were involved in myogenesis [36][37][38][39][40][41][42][43]. In our study, we highlighted that circBBS9 was a potential biomarker of aging-associated muscle dysfunction and may potentially mediate the amelioration effects exerted by exercise.…”

An integration analysis based on genomic, transcriptomic and QTX information reveals credible candidate genes for fat‐related traits in pigs

“…Since longer QTL will introduce more false positive results, we assumed that 1 Mbp on either side of the peak (center of the QTL) would be adequate to encompass the underlying genes or polymorphisms responsible for the QTL (Shen et al 2019) and cut QTL that are longer than 2 Mbp down to 2 Mbp. The adjusted QTL and the QTL less than 2 Mbp were considered as the effective QTL regions and were used for subsequent analyses.…”

“…2018; Shen et al . 2019), but no deep integration analysis of QTXs information in pigs has been reported. In this study, we focused on the fat‐related traits in pig, and constructed a unified physical map.…”