Assessment of different enrichment methods revealed the optimal approach to identify bovine circRnas
Although circular RNAs (circRNAs) play important roles in regulating gene expression, the understanding of circRNAs in livestock animals is scarce due to the significant challenge to characterize them from a biological sample. In this study, we assessed the outcomes of bovine circRNA identification...
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2024-12-01
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| Series: | RNA Biology |
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| Online Access: | https://www.tandfonline.com/doi/10.1080/15476286.2024.2356334 |
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| author | Yixin Wang Jian Wang Robert J. Gruninger Tim A. McAllister Mingzhou Li Le Luo Guan |
| author_facet | Yixin Wang Jian Wang Robert J. Gruninger Tim A. McAllister Mingzhou Li Le Luo Guan |
| author_sort | Yixin Wang |
| collection | DOAJ |
| description | Although circular RNAs (circRNAs) play important roles in regulating gene expression, the understanding of circRNAs in livestock animals is scarce due to the significant challenge to characterize them from a biological sample. In this study, we assessed the outcomes of bovine circRNA identification using six enrichment approaches with the combination of ribosomal RNAs removal (Ribo); linear RNAs degradation (R); linear RNAs and RNAs with structured 3′ ends degradation (RTP); ribosomal RNAs coupled with linear RNAs elimination (Ribo-R); ribosomal RNA, linear RNAs and RNAs with poly (A) tailing elimination (Ribo-RP); and ribosomal RNA, linear RNAs and RNAs with structured 3′ ends elimination (Ribo-RTP), respectively. RNA-sequencing analysis revealed that different approaches led to varied ratio of uniquely mapped reads, false-positive rate of identifying circRNAs, and the number of circRNAs per million clean reads (Padj <0.05). Out of 2,285 and 2,939 highly confident circRNAs identified in liver and rumen tissues, respectively, 308 and 260 were commonly identified from five methods, with Ribo-RTP method identified the highest number of circRNAs. Besides, 507 of 4,051 identified bovine highly confident circRNAs had shared splicing sites with human circRNAs. The findings from this work provide optimized methods to identify bovine circRNAs from cattle tissues for downstream research of their biological roles in cattle. |
| format | Article |
| id | doaj-art-37fc483d9e434ff0ae610fc30e70dde6 |
| institution | Kabale University |
| issn | 1547-6286 1555-8584 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | RNA Biology |
| spelling | doaj-art-37fc483d9e434ff0ae610fc30e70dde62025-02-05T05:42:20ZengTaylor & Francis GroupRNA Biology1547-62861555-85842024-12-0121162163310.1080/15476286.2024.2356334Assessment of different enrichment methods revealed the optimal approach to identify bovine circRnasYixin Wang0Jian Wang1Robert J. Gruninger2Tim A. McAllister3Mingzhou Li4Le Luo Guan5Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, ChinaDepartment of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, CanadaLethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, CanadaLethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, CanadaLivestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, ChinaDepartment of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, CanadaAlthough circular RNAs (circRNAs) play important roles in regulating gene expression, the understanding of circRNAs in livestock animals is scarce due to the significant challenge to characterize them from a biological sample. In this study, we assessed the outcomes of bovine circRNA identification using six enrichment approaches with the combination of ribosomal RNAs removal (Ribo); linear RNAs degradation (R); linear RNAs and RNAs with structured 3′ ends degradation (RTP); ribosomal RNAs coupled with linear RNAs elimination (Ribo-R); ribosomal RNA, linear RNAs and RNAs with poly (A) tailing elimination (Ribo-RP); and ribosomal RNA, linear RNAs and RNAs with structured 3′ ends elimination (Ribo-RTP), respectively. RNA-sequencing analysis revealed that different approaches led to varied ratio of uniquely mapped reads, false-positive rate of identifying circRNAs, and the number of circRNAs per million clean reads (Padj <0.05). Out of 2,285 and 2,939 highly confident circRNAs identified in liver and rumen tissues, respectively, 308 and 260 were commonly identified from five methods, with Ribo-RTP method identified the highest number of circRNAs. Besides, 507 of 4,051 identified bovine highly confident circRNAs had shared splicing sites with human circRNAs. The findings from this work provide optimized methods to identify bovine circRNAs from cattle tissues for downstream research of their biological roles in cattle.https://www.tandfonline.com/doi/10.1080/15476286.2024.2356334circRNAsenrichment methodsbioinformatic pipelinebovine specific circRNAsbovine tissues |
| spellingShingle | Yixin Wang Jian Wang Robert J. Gruninger Tim A. McAllister Mingzhou Li Le Luo Guan Assessment of different enrichment methods revealed the optimal approach to identify bovine circRnas RNA Biology circRNAs enrichment methods bioinformatic pipeline bovine specific circRNAs bovine tissues |
| title | Assessment of different enrichment methods revealed the optimal approach to identify bovine circRnas |
| title_full | Assessment of different enrichment methods revealed the optimal approach to identify bovine circRnas |
| title_fullStr | Assessment of different enrichment methods revealed the optimal approach to identify bovine circRnas |
| title_full_unstemmed | Assessment of different enrichment methods revealed the optimal approach to identify bovine circRnas |
| title_short | Assessment of different enrichment methods revealed the optimal approach to identify bovine circRnas |
| title_sort | assessment of different enrichment methods revealed the optimal approach to identify bovine circrnas |
| topic | circRNAs enrichment methods bioinformatic pipeline bovine specific circRNAs bovine tissues |
| url | https://www.tandfonline.com/doi/10.1080/15476286.2024.2356334 |
| work_keys_str_mv | AT yixinwang assessmentofdifferentenrichmentmethodsrevealedtheoptimalapproachtoidentifybovinecircrnas AT jianwang assessmentofdifferentenrichmentmethodsrevealedtheoptimalapproachtoidentifybovinecircrnas AT robertjgruninger assessmentofdifferentenrichmentmethodsrevealedtheoptimalapproachtoidentifybovinecircrnas AT timamcallister assessmentofdifferentenrichmentmethodsrevealedtheoptimalapproachtoidentifybovinecircrnas AT mingzhouli assessmentofdifferentenrichmentmethodsrevealedtheoptimalapproachtoidentifybovinecircrnas AT leluoguan assessmentofdifferentenrichmentmethodsrevealedtheoptimalapproachtoidentifybovinecircrnas |