AUTHOR=Yu Zonggang , Xu Xueli , Ai Nini , Wang Kaiming , Zhang Peiwen , Li Xintong , LiuFu Sui , Liu Xiaolin , Jiang Jun , Gu Jingjing , Gao Ning , Ma Haiming 

TITLE=Integrated analysis of circRNA, lncRNA, miRNA and mRNA to reveal the ceRNA regulatory network of postnatal skeletal muscle development in Ningxiang pig

JOURNAL=Frontiers in Cell and Developmental Biology

VOLUME=Volume 11 - 2023

YEAR=2023

URL=https://www.frontiersin.org/journals/cell-and-developmental-biology/articles/10.3389/fcell.2023.1185823

DOI=10.3389/fcell.2023.1185823

ISSN=2296-634X

ABSTRACT=The development of skeletal muscle is regulated by regulatory factors of genes and ncRNAs. In this study, the histological analysis and whole transcriptome sequencing of the longissimus dorsi muscle of Ningxiang male pig at four growth stages (30, 90, 150 and 210 days after birth, n=3) revealed the regularity of muscle fiber type transformation of the skeletal muscle, explored the expression regularity of various RNAs involved in the muscle fiber transformation of skeletal muscle, and constructed a competing endogenous RNA (ceRNA) regulatory network of circRNA/lncRNA-miRNA-mRNA. Histomorphological analysis showed that the diameter of muscle fiber reached the maximum at 150 days and then stopped increasing. The slow muscle fiber transformation showed a pattern of first decreasing and then increasing. 29963 circRNA, 2683 lncRNA, 986 miRNA and 22411 mRNA were identified by whole transcriptome sequencing. Further, 642 differentially expressed circRNA (DEc), 505 differentially expressed lncRNA (DEl), 316 differentially expressed miRNA (DEmi) and 6090 differentially expressed mRNA (DEm) were identified by differential expression analysis. Functions of differentially expressed mRNA were identified by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Through GO enrichment analysis, 40 known genes and 6 new genes were related to skeletal muscle development. KEGG found that these skeletal muscle-related genes affects skeletal muscle development through MAPK, FoxO, Hedgehog, PI3K-Akt, Notch, VEGF and other signaling pathways. Through protein-protein interaction (PPI) and transcription factor prediction (TFP), the action mode of skeletal muscle-related genes was explored. PPI analysis showed that there were stable interactions among 19 proteins, while TF analysis predicted 22 transcription factors such as HMG20B, MYF6, MYOD1 and MYOG and 12 of the 19 interacting proteins were transcription factors. The regulatory network of ceRNA related to skeletal muscle development was constructed based on the correlation of various RNA expression levels and the targeted binding characteristics with miRNA. The regulatory network included 31 DEms, 59 miRNAs, 667 circRNAs and 224 lncRNAs. This study revealed the role of ceRNA regulatory network in the transformation of skeletal muscle fiber types in Ningxiang pigs and improved our understanding of ceRNA regulatory network in the development of skeletal muscle in Ningxiang pigs.