Comprehensive Analysis of CircRNA Expression Profiles in Multiple Tissues of Pigs
-
Published:2023-11-11
Issue:22
Volume:24
Page:16205
-
ISSN:1422-0067
-
Container-title:International Journal of Molecular Sciences
-
language:en
-
Short-container-title:IJMS
Author:
Shen Qingpeng1ORCID, Gong Wentao1, Pan Xiangchun1, Cai Jiali1, Jiang Yao12, He Mingran1, Zhao Shanghui1, Li Yipeng1, Yuan Xiaolong1ORCID, Li Jiaqi1
Affiliation:
1. Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China 2. School of Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, WA 6149, Australia
Abstract
Circular RNAs (circRNAs) are a class of non-coding RNAs with diverse functions, and previous studies have reported that circRNAs are involved in the growth and development of pigs. However, studies about porcine circRNAs over the past few years have focused on a limited number of tissues. Based on 215 publicly available RNA sequencing (RNA-seq) samples, we conducted a comprehensive analysis of circRNAs in nine pig tissues, namely, the gallbladder, heart, liver, longissimus dorsi, lung, ovary, pituitary, skeletal muscle, and spleen. Here, we identified a total of 82,528 circRNAs and discovered 3818 novel circRNAs that were not reported in the CircAtlas database. Moreover, we obtained 492 housekeeping circRNAs and 3489 tissue-specific circRNAs. The housekeeping circRNAs were enriched in signaling pathways regulating basic biological tissue activities, such as chromatin remodeling, nuclear-transcribed mRNA catabolic process, and protein methylation. The tissue-specific circRNAs were enriched in signaling pathways related to tissue-specific functions, such as muscle system process in skeletal muscle, cilium organization in pituitary, and cortical cytoskeleton in ovary. Through weighted gene co-expression network analysis, we identified 14 modules comprising 1377 hub circRNAs. Additionally, we explored circRNA–miRNA–mRNA networks to elucidate the interaction relationships between tissue-specific circRNAs and tissue-specific genes. Furthermore, our conservation analysis revealed that 19.29% of circRNAs in pigs shared homologous positions with their counterparts in humans. In summary, this extensive profiling of housekeeping, tissue-specific, and co-expressed circRNAs provides valuable insights into understanding the molecular mechanisms of pig transcriptional expression, ultimately deepening our understanding of genetic and biological processes.
Funder
Key R&D Program of Guangdong Province Project National Natural Science Foundation of China Earmarked fund for China Agriculture Research System Guangdong Basic and Applied Basic Research Foundation Breed Industry Innovation Park of Guangdong Xiaoerhua Pig
Subject
Inorganic Chemistry,Organic Chemistry,Physical and Theoretical Chemistry,Computer Science Applications,Spectroscopy,Molecular Biology,General Medicine,Catalysis
Reference72 articles.
1. Viroids are single-strandedcovalently closed circular RNA molecules existing as highly base-paired rod-like structures;Sanger;Proc. Natl. Acad. Sci. USA,1976 2. Translation and functional roles of circular RNAs in human cancer;Lei;Mol. Cancer,2020 3. Circular RNAs in renal cell carcinoma: Implications for tumorigenesis, diagnosis, and therapy;Wang;Mol. Cancer,2020 4. Salzman, J., Gawad, C., Wang, P.L., Lacayo, N., and Brown, P.O. (2012). Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS ONE, 7. 5. Foxo3 circular RNA retards cell cycle progression via forming ternary complexes with p21 and CDK2;Du;Nucleic Acids Res.,2016
|
|