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Journal article
Comprehensive Analysis of CircRNA Expression Profiles in Multiple Tissues of Pigs
International journal of molecular sciences, Vol.24(22), 16205
2023
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.
Details
- Title
- Comprehensive Analysis of CircRNA Expression Profiles in Multiple Tissues of Pigs
- Authors/Creators
- Qingpeng Shen - South China Agricultural UniversityWentao Gong - South China Agricultural UniversityXiangchun Pan - South China Agricultural UniversityJiali Cai - South China Agricultural UniversityYao Jiang - Murdoch UniversityMingran He - South China Agricultural UniversityShanghui ZhaoYipeng Li - South China Agricultural UniversityXiaolong Yuan - South China Agricultural UniversityJiaqi Li - South China Agricultural University
- Publication Details
- International journal of molecular sciences, Vol.24(22), 16205
- Publisher
- MDPI AG
- Identifiers
- 991005618765007891
- Copyright
- © 2023 by the authors.
- Murdoch Affiliation
- School of Medical, Molecular and Forensic Sciences
- Language
- English
- Resource Type
- Journal article
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