Characterization of lncRNA/circRNA-miRNA-mRNA network to reveal potential functional ceRNAs in the skeletal muscle of chicken

Abstract

Skeletal muscle, comprising approximately 40% of body mass, is a highly complex and heterogeneous tissue serving a multitude of functions in the organism. Non-coding RNAs (ncRNAs) are known to participate in skeletal muscle development as critical regulators. However, the regulatory mechanisms of ncRNAs on chicken muscle traits are not well understood. In the present study, we collected the leg muscle from male embryos of Tibetan chicken at embryonic (E) 10 and E18 for RNA sequencing. A total of 6,583 differentially expressed mRNAs (DEMs) including 3,055 down-regulated and 3,528 up-regulated were identified in E18. We identified 695 differentially expressed lncRNAs (DELs) (187 down-regulated and 508 up-regulated) and 1,906 differentially expressed circRNAs (DECs) (1,224 down-regulated and 682 up-regulated) in E18. Among the 130 differentially expressed miRNAs (DEMIs), 59 were up-regulated and 71 were down-regulated in E18. Numerous DEMs and target genes for miRNAs/lncRNAs were significantly enriched in the muscle system process and cell cycle. We constructed a miRNA-gene-pathway network by considering target relationships between genes related to skeletal muscle development and miRNAs. A competing endogenous RNA (ceRNA) network was also constructed by integrating competing relationships between DEMs, DELs, and DECs. Several DELs and DECs were predicted to regulate the ADRA1B, ATP2A2, ATP2B1, CACNA1S, CACNB4, MYLK2, and ROCK2 genes. We discovered the crosstalk between the ncRNAs and their competing mRNAs, which provides insights into ceRNA function and mechanisms in the skeletal muscle development of chicken.

Genome-wide characteristics and potential functions of circular RNAs from the embryo muscle development in Chengkou mountain chicken

“…The stained muscle sections indicated that the embryonic muscle development pattern of the Chengkou mountain chicken closely resembled that of the Tibetan chicken and other local breeds in China ( 27 , 28 ). During E12, the muscle fibers were intermixed, and their distinct boundaries were indiscernible.…”

Non-coding RNA regulation of Magang geese skeletal muscle maturation via the MAPK signaling pathway

“…The leg muscles of geese are the main components of their skeletal muscles, and the production of goose meat is closely related to the growth and development of skeletal muscles (Pan et al, 2022). In this study, we investigated the regulatory mechanisms underlying skeletal muscle maturation by collecting samples of leg skeletal Frontiers in Physiology frontiersin.org muscles from Magang geese at 3 days and 3 months of age.…”

Transcriptome Sequencing Analysis of circRNA in Skeletal Muscle between Fast- and Slow-Growing Chickens at Embryonic Stages

“…Some KEGG pathways for host genes of DECs in the experiment were the same as those of other studies. Pan et al [ 42 ] collected the leg muscle from male embryos of Tibetan chicken at embryonic (E) days 10 and 18 for RNA sequencing, and KEGG results for the host genes of DECs revealed that the enriched pathways involved Wnt signaling pathway and MAPK signaling pathway. The two terms were also enriched in the top 20 KEGG pathways in S14 vs. F14.…”