Abstract
Growing evidence has demonstrated the emerging role of long non-coding RNA as competitive endogenous RNA (ceRNA) in regulating skeletal muscle development. However, the mechanism of ceRNA regulated by lncRNA in pigeon skeletal muscle development remains unclear. To reveal the function and regulatory mechanisms of lncRNA, we first analyzed the expression profiles of lncRNA, microRNA (miRNA), and mRNA during the development of pigeon skeletal muscle using high-throughput sequencing. We then constructed a lncRNA–miRNA–mRNA ceRNA network based on differentially expressed (DE) lncRNAs, miRNAs, and mRNAs according to the ceRNA hypothesis. Functional enrichment and short time-series expression miner (STEM) analysis were performed to explore the function of the ceRNA network. Hub lncRNA–miRNA–mRNA interactions were identified by connectivity degree and validated using dual-luciferase activity assay. The results showed that a total of 1625 DE lncRNAs, 11,311 DE mRNAs, and 573 DE miRNAs were identified. A ceRNA network containing 9120 lncRNA–miRNA–mRNA interactions was constructed. STEM analysis indicated that the function of the lncRNA-associated ceRNA network might be developmental specific. Functional enrichment analysis identified potential pathways regulating pigeon skeletal muscle development, such as cell cycle and MAPK signaling. Based on the connectivity degree, lncRNAs TCONS_00066712, TCONS_00026594, TCONS_00001557, TCONS_00001553, and TCONS_00003307 were identified as hub genes in the ceRNA network. lncRNA TCONS_00026594 might regulate the FSHD region gene 1 (FRG1)/ SRC proto-oncogene, non-receptor tyrosine kinase (SRC) by sponge adsorption of cli-miR-1a-3p to affect the development of pigeon skeletal muscle. Our findings provide a data basis for in-depth elucidation of the lncRNA-associated ceRNA mechanism underlying pigeon skeletal muscle development.
Highlights
Over the past decades, breeders and growers have devoted themselves to increasing the growth rate of birds, feed efficiency, and size of breast muscle to meet the global increasing demand for poultry meat [1]
Our study aims to construct a long non-coding RNA (lncRNA)-associated competitive endogenous RNA (ceRNA) network and thereby identify key lncRNA–miRNA–mRNA interactions involved in pigeon skeletal muscle development, which will enhance our understanding of the molecular mechanisms underlying pigeon skeletal muscle myogenesis
By RNA sequencing (RNA-seq) and miRNA-seq, a total of 5076 lncRNAs, 2362 miRNAs, and 32,527 mRNAs were detected in pigeon skeletal muscle samples (Table S4)
Summary
Breeders and growers have devoted themselves to increasing the growth rate of birds, feed efficiency, and size of breast muscle to meet the global increasing demand for poultry meat [1]. Poultry meat has become the most consumed and affordable type of meat among animal sources, worldwide [2]. By 2026, poultry meat is expected to account for 45% of global meat consumption [3]. Pigeon meat is consumed as high-quality and nutritional poultry meat and is gaining popularity among consumers, globally [4]. Pigeon meat is characterized by a high nutritive value with low cholesterol and relatively high protein content compared with other poultry, and it can be used as a valuable, inclusive component of the human diet [5]. The pigeon industry is focusing on the increasing growth rate of pigeons to enhance the industry’s capacity to increase production and profitability [6]
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