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Comprehensive Analysis of CircRNA Expression Profiles in Multiple Tissues of Pigs
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 2...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10671760/ https://www.ncbi.nlm.nih.gov/pubmed/38003395 http://dx.doi.org/10.3390/ijms242216205 |
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author | Shen, Qingpeng Gong, Wentao Pan, Xiangchun Cai, Jiali Jiang, Yao He, Mingran Zhao, Shanghui Li, Yipeng Yuan, Xiaolong Li, Jiaqi |
author_facet | Shen, Qingpeng Gong, Wentao Pan, Xiangchun Cai, Jiali Jiang, Yao He, Mingran Zhao, Shanghui Li, Yipeng Yuan, Xiaolong Li, Jiaqi |
author_sort | Shen, Qingpeng |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-10671760 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-106717602023-11-11 Comprehensive Analysis of CircRNA Expression Profiles in Multiple Tissues of Pigs Shen, Qingpeng Gong, Wentao Pan, Xiangchun Cai, Jiali Jiang, Yao He, Mingran Zhao, Shanghui Li, Yipeng Yuan, Xiaolong Li, Jiaqi Int J Mol Sci Article 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. MDPI 2023-11-11 /pmc/articles/PMC10671760/ /pubmed/38003395 http://dx.doi.org/10.3390/ijms242216205 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Shen, Qingpeng Gong, Wentao Pan, Xiangchun Cai, Jiali Jiang, Yao He, Mingran Zhao, Shanghui Li, Yipeng Yuan, Xiaolong Li, Jiaqi Comprehensive Analysis of CircRNA Expression Profiles in Multiple Tissues of Pigs |
title | Comprehensive Analysis of CircRNA Expression Profiles in Multiple Tissues of Pigs |
title_full | Comprehensive Analysis of CircRNA Expression Profiles in Multiple Tissues of Pigs |
title_fullStr | Comprehensive Analysis of CircRNA Expression Profiles in Multiple Tissues of Pigs |
title_full_unstemmed | Comprehensive Analysis of CircRNA Expression Profiles in Multiple Tissues of Pigs |
title_short | Comprehensive Analysis of CircRNA Expression Profiles in Multiple Tissues of Pigs |
title_sort | comprehensive analysis of circrna expression profiles in multiple tissues of pigs |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10671760/ https://www.ncbi.nlm.nih.gov/pubmed/38003395 http://dx.doi.org/10.3390/ijms242216205 |
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