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

• DOI: 10.3389/fcell.2023.1185823
• Publication Date: 2023-07-03T06:04:11Z
• Authors: Zonggang Yu; Xueli Xu; Nini Ai; Kaiming Wang; Peiwen Zhang; Xintong Li; Sui LiuFu; Xiaolin Liu; Jun Jiang; Jingjing Gu; Ning Gao; Haiming Ma
• Keywords: Competing Endogenous RNA; KEGG; Gene regulatory network

Introduction: The development of skeletal muscle is regulated by regulatory factors genes and non-coding RNAs (ncRNAs). Methods: objective this study was to understand the transformation fiber type in longissimus dorsi male Ningxiang pigs at four different growth stages (30, 90, 150, 210 days after birth, n = 3) histological analysis whole transcriptome sequencing. Additionally, investigated expression patterns various involved constructed a network for competing endogenous RNA (ceRNA) that includes circular (circRNA)/long (lncRNA)-microRNA (miRNA)-messenger (mRNA). Results: Histomorphology showed diameter reached its maximum 150 birth. slow pattern initial decrease followed an increase. 29,963 circRNAs, 2,683 lncRNAs, 986 miRNAs 22,411 mRNAs with level ≥0 were identified Furthermore, 642 differentially expressed circRNAs (DEc), 505 lncRNAs (DEl), 316 (DEmi) 6,090 (DEm) differential analysis. Functions mRNA gene ontology (GO) Kyoto Encyclopedia Genes Genomes (KEGG). GO enrichment indicates 40 known 6 new are associated development. KEGG shows these regulate via MAPK, FoxO, Hedgehog, PI3K-Akt, Notch, VEGF other signaling pathways. Through protein-protein interaction (PPI) transcription factor prediction (TFP), action mode muscle-related explored. PPI there stable interactions among 19 proteins, meanwhile, TFP predicted 22 such as HMG20B, MYF6, MYOD1 MYOG, 12 interacting proteins factors. ceRNA related based on correlation levels targeted binding characteristics miRNA. included 31 DEms, 59 miRNAs, 667 224 lncRNAs. conclusion: Overall, revealed role types pigs, which contributes understanding during period.