Genome-wide analysis of circRNA regulation during spleen development of Chinese indigenous breed Meishan pigs
Abstract Background Numerous circular RNAs (circRNAs) have been recently identified in porcine tissues and cell types. Nevertheless, their significance in porcine spleen development is yet unelucidated. Herein, we reported an extensive overlook of circRNA expression profile during spleen development...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-08-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-023-09612-x |
| _version_ | 1797577982095654912 |
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| author | Yifu Wang Jinhua Cheng Chao Xu Jian Jin Wenbin Bao Shenglong Wu Zhengchang Wu |
| author_facet | Yifu Wang Jinhua Cheng Chao Xu Jian Jin Wenbin Bao Shenglong Wu Zhengchang Wu |
| author_sort | Yifu Wang |
| collection | DOAJ |
| description | Abstract Background Numerous circular RNAs (circRNAs) have been recently identified in porcine tissues and cell types. Nevertheless, their significance in porcine spleen development is yet unelucidated. Herein, we reported an extensive overlook of circRNA expression profile during spleen development in Meishan pigs. Results Overall, 39,641 circRNAs were identified from 6,914 host genes. Among them, many circRNAs are up- or down-regulated at different time points of pig spleen development. Using WGCNA analysis, we revealed two essential modules for protein-coding genes and circRNAs. Subsequent correlation analysis revealed 67 circRNAs/co-expressed genes that participated in immnue-associated networks. Furthermore, a competing endogenous RNA (ceRNA) network analysis of circRNAs revealed that 12 circRNAs modulated CD226, MBD2, SAMD3, SIT1, SRP14, SYTL3 gene expressions via acting as miRNA sponges. Moreover, the circRNA_21767/miR-202-3p axis regulated SIT1 expression in a ceRNA manner, which is critical for the immune-based regulation of spleen development in Meishan pigs. Conclusions Overall, our results demonstrated that the circRNAs were differentially expressed during different stages of porcine spleen development, meanwhile the circRNAs interacted with immune-related genes in a ceRNA-based fashion. Moreover, we presented biomedical researchers with RNAseqTools, a user-friendly and powerful software for the visualization of transcriptome profile data. |
| first_indexed | 2024-03-10T22:15:50Z |
| format | Article |
| id | doaj.art-de06b9555c91458da262b061d311cd2f |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-10T22:15:50Z |
| publishDate | 2023-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-de06b9555c91458da262b061d311cd2f2023-11-19T12:27:18ZengBMCBMC Genomics1471-21642023-08-0124111410.1186/s12864-023-09612-xGenome-wide analysis of circRNA regulation during spleen development of Chinese indigenous breed Meishan pigsYifu Wang0Jinhua Cheng1Chao Xu2Jian Jin3Wenbin Bao4Shenglong Wu5Zhengchang Wu6College of Animal Science and Technology, Yangzhou UniversityInstitute of Animal Science, Jiangsu Academy of Agricultural SciencesCollege of Animal Science and Technology, Yangzhou UniversityInstitute of Comparative Medicine, College of Veterinary Medicine, Yangzhou UniversityCollege of Animal Science and Technology, Yangzhou UniversityCollege of Animal Science and Technology, Yangzhou UniversityCollege of Animal Science and Technology, Yangzhou UniversityAbstract Background Numerous circular RNAs (circRNAs) have been recently identified in porcine tissues and cell types. Nevertheless, their significance in porcine spleen development is yet unelucidated. Herein, we reported an extensive overlook of circRNA expression profile during spleen development in Meishan pigs. Results Overall, 39,641 circRNAs were identified from 6,914 host genes. Among them, many circRNAs are up- or down-regulated at different time points of pig spleen development. Using WGCNA analysis, we revealed two essential modules for protein-coding genes and circRNAs. Subsequent correlation analysis revealed 67 circRNAs/co-expressed genes that participated in immnue-associated networks. Furthermore, a competing endogenous RNA (ceRNA) network analysis of circRNAs revealed that 12 circRNAs modulated CD226, MBD2, SAMD3, SIT1, SRP14, SYTL3 gene expressions via acting as miRNA sponges. Moreover, the circRNA_21767/miR-202-3p axis regulated SIT1 expression in a ceRNA manner, which is critical for the immune-based regulation of spleen development in Meishan pigs. Conclusions Overall, our results demonstrated that the circRNAs were differentially expressed during different stages of porcine spleen development, meanwhile the circRNAs interacted with immune-related genes in a ceRNA-based fashion. Moreover, we presented biomedical researchers with RNAseqTools, a user-friendly and powerful software for the visualization of transcriptome profile data.https://doi.org/10.1186/s12864-023-09612-xPorcineCircRNAsSpleenDevelopment |
| spellingShingle | Yifu Wang Jinhua Cheng Chao Xu Jian Jin Wenbin Bao Shenglong Wu Zhengchang Wu Genome-wide analysis of circRNA regulation during spleen development of Chinese indigenous breed Meishan pigs BMC Genomics Porcine CircRNAs Spleen Development |
| title | Genome-wide analysis of circRNA regulation during spleen development of Chinese indigenous breed Meishan pigs |
| title_full | Genome-wide analysis of circRNA regulation during spleen development of Chinese indigenous breed Meishan pigs |
| title_fullStr | Genome-wide analysis of circRNA regulation during spleen development of Chinese indigenous breed Meishan pigs |
| title_full_unstemmed | Genome-wide analysis of circRNA regulation during spleen development of Chinese indigenous breed Meishan pigs |
| title_short | Genome-wide analysis of circRNA regulation during spleen development of Chinese indigenous breed Meishan pigs |
| title_sort | genome wide analysis of circrna regulation during spleen development of chinese indigenous breed meishan pigs |
| topic | Porcine CircRNAs Spleen Development |
| url | https://doi.org/10.1186/s12864-023-09612-x |
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