Conserved A-to-I RNA editing with non-conserved recoding expands the candidates of functional editing sites
Adenosine-to-inosine (A-to-I) RNA editing recodes the genome and confers flexibility for the organisms to adapt to the environment. It is believed that RNA recoding sites are well suited for facilitating adaptive evolution by increasing the proteomic diversity in a temporal-spatial manner. The funct...
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2024-12-01
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| Series: | Fly |
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| Online Access: | https://www.tandfonline.com/doi/10.1080/19336934.2024.2367359 |
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| author | Yuange Duan Ling Ma Tianyou Zhao Jiyao Liu Caiqing Zheng Fan Song Li Tian Wanzhi Cai Hu Li |
| author_facet | Yuange Duan Ling Ma Tianyou Zhao Jiyao Liu Caiqing Zheng Fan Song Li Tian Wanzhi Cai Hu Li |
| author_sort | Yuange Duan |
| collection | DOAJ |
| description | Adenosine-to-inosine (A-to-I) RNA editing recodes the genome and confers flexibility for the organisms to adapt to the environment. It is believed that RNA recoding sites are well suited for facilitating adaptive evolution by increasing the proteomic diversity in a temporal-spatial manner. The function and essentiality of a few conserved recoding sites are recognized. However, the experimentally discovered functional sites only make up a small corner of the total sites, and there is still the need to expand the repertoire of such functional sites with bioinformatic approaches. In this study, we define a new category of RNA editing sites termed ‘conserved editing with non-conserved recoding’ and systematically identify such sites in Drosophila editomes, figuring out their selection pressure and signals of adaptation at inter-species and intra-species levels. Surprisingly, conserved editing sites with non-conserved recoding are not suppressed and are even slightly overrepresented in Drosophila. DNA mutations leading to such cases are also favoured during evolution, suggesting that the function of those recoding events in different species might be diverged, specialized, and maintained. Finally, structural prediction suggests that such recoding in potassium channel Shab might increase ion permeability and compensate the effect of low temperature. In conclusion, conserved editing with non-conserved recoding might be functional as well. Our study provides novel aspects in considering the adaptive evolution of RNA editing sites and meanwhile expands the candidates of functional recoding sites for future validation. |
| format | Article |
| id | doaj-art-71404b834a8a4dbe9274581ea08878f4 |
| institution | OA Journals |
| issn | 1933-6934 1933-6942 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Fly |
| spelling | doaj-art-71404b834a8a4dbe9274581ea08878f42025-08-20T02:13:47ZengTaylor & Francis GroupFly1933-69341933-69422024-12-0118110.1080/19336934.2024.2367359Conserved A-to-I RNA editing with non-conserved recoding expands the candidates of functional editing sitesYuange DuanLing MaTianyou ZhaoJiyao Liu0Caiqing Zheng1Fan Song2Li Tian3Wanzhi Cai4Hu Li5Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, ChinaDepartment of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, ChinaDepartment of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, ChinaDepartment of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, ChinaDepartment of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, ChinaDepartment of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, ChinaAdenosine-to-inosine (A-to-I) RNA editing recodes the genome and confers flexibility for the organisms to adapt to the environment. It is believed that RNA recoding sites are well suited for facilitating adaptive evolution by increasing the proteomic diversity in a temporal-spatial manner. The function and essentiality of a few conserved recoding sites are recognized. However, the experimentally discovered functional sites only make up a small corner of the total sites, and there is still the need to expand the repertoire of such functional sites with bioinformatic approaches. In this study, we define a new category of RNA editing sites termed ‘conserved editing with non-conserved recoding’ and systematically identify such sites in Drosophila editomes, figuring out their selection pressure and signals of adaptation at inter-species and intra-species levels. Surprisingly, conserved editing sites with non-conserved recoding are not suppressed and are even slightly overrepresented in Drosophila. DNA mutations leading to such cases are also favoured during evolution, suggesting that the function of those recoding events in different species might be diverged, specialized, and maintained. Finally, structural prediction suggests that such recoding in potassium channel Shab might increase ion permeability and compensate the effect of low temperature. In conclusion, conserved editing with non-conserved recoding might be functional as well. Our study provides novel aspects in considering the adaptive evolution of RNA editing sites and meanwhile expands the candidates of functional recoding sites for future validation.https://www.tandfonline.com/doi/10.1080/19336934.2024.2367359A-to-I RNA editingconservedrecodingselectionevolution |
| spellingShingle | Yuange Duan Ling Ma Tianyou Zhao Jiyao Liu Caiqing Zheng Fan Song Li Tian Wanzhi Cai Hu Li Conserved A-to-I RNA editing with non-conserved recoding expands the candidates of functional editing sites Fly A-to-I RNA editing conserved recoding selection evolution |
| title | Conserved A-to-I RNA editing with non-conserved recoding expands the candidates of functional editing sites |
| title_full | Conserved A-to-I RNA editing with non-conserved recoding expands the candidates of functional editing sites |
| title_fullStr | Conserved A-to-I RNA editing with non-conserved recoding expands the candidates of functional editing sites |
| title_full_unstemmed | Conserved A-to-I RNA editing with non-conserved recoding expands the candidates of functional editing sites |
| title_short | Conserved A-to-I RNA editing with non-conserved recoding expands the candidates of functional editing sites |
| title_sort | conserved a to i rna editing with non conserved recoding expands the candidates of functional editing sites |
| topic | A-to-I RNA editing conserved recoding selection evolution |
| url | https://www.tandfonline.com/doi/10.1080/19336934.2024.2367359 |
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