Narrowing down the candidates of beneficial A-to-I RNA editing by comparing the recoding sites with uneditable counterparts
Adar-mediated adenosine-to-inosine (A-to-I) RNA editing mainly occurs in nucleus and diversifies the transcriptome in a flexible manner. It has been a challenging task to identify beneficial editing sites from the sea of total editing events. The functional Ser>Gly auto-recoding site in insect Ad...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2024-12-01
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| Series: | Nucleus |
| Subjects: | |
| Online Access: | https://www.tandfonline.com/doi/10.1080/19491034.2024.2304503 |
| _version_ | 1826945161817489408 |
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| author | Tianyou Zhao Ling Ma Shiwen Xu Wanzhi Cai Hu Li Yuange Duan |
| author_facet | Tianyou Zhao Ling Ma Shiwen Xu Wanzhi Cai Hu Li Yuange Duan |
| author_sort | Tianyou Zhao |
| collection | DOAJ |
| description | Adar-mediated adenosine-to-inosine (A-to-I) RNA editing mainly occurs in nucleus and diversifies the transcriptome in a flexible manner. It has been a challenging task to identify beneficial editing sites from the sea of total editing events. The functional Ser>Gly auto-recoding site in insect Adar gene has uneditable Ser codons in ancestral nodes, indicating the selective advantage to having an editable status. Here, we extended this case study to more metazoan species, and also looked for all Drosophila recoding events with potential uneditable synonymous codons. Interestingly, in D. melanogaster, the abundant nonsynonymous editing is enriched in the codons that have uneditable counterparts, but the Adar Ser>Gly case suggests that the editable orthologous codons in other species are not necessarily edited. The use of editable versus ancestral uneditable codon is a smart way to infer the selective advantage of RNA editing, and priority might be given to these editing sites for functional studies due to the feasibility to construct an uneditable allele. Our study proposes an idea to narrow down the candidates of beneficial recoding sites. Meanwhile, we stress that the matched transcriptomes are needed to verify the conservation of editing events during evolution. |
| first_indexed | 2024-03-08T09:43:04Z |
| format | Article |
| id | doaj.art-bfedeb02768d4552a57d0fee6f8fa8c1 |
| institution | Directory Open Access Journal |
| issn | 1949-1034 1949-1042 |
| language | English |
| last_indexed | 2025-02-17T20:50:26Z |
| publishDate | 2024-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Nucleus |
| spelling | doaj.art-bfedeb02768d4552a57d0fee6f8fa8c12024-12-09T07:27:13ZengTaylor & Francis GroupNucleus1949-10341949-10422024-12-0115110.1080/19491034.2024.2304503Narrowing down the candidates of beneficial A-to-I RNA editing by comparing the recoding sites with uneditable counterpartsTianyou Zhao0Ling Ma1Shiwen Xu2Wanzhi Cai3Hu Li4Yuange Duan5Department 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, ChinaAdar-mediated adenosine-to-inosine (A-to-I) RNA editing mainly occurs in nucleus and diversifies the transcriptome in a flexible manner. It has been a challenging task to identify beneficial editing sites from the sea of total editing events. The functional Ser>Gly auto-recoding site in insect Adar gene has uneditable Ser codons in ancestral nodes, indicating the selective advantage to having an editable status. Here, we extended this case study to more metazoan species, and also looked for all Drosophila recoding events with potential uneditable synonymous codons. Interestingly, in D. melanogaster, the abundant nonsynonymous editing is enriched in the codons that have uneditable counterparts, but the Adar Ser>Gly case suggests that the editable orthologous codons in other species are not necessarily edited. The use of editable versus ancestral uneditable codon is a smart way to infer the selective advantage of RNA editing, and priority might be given to these editing sites for functional studies due to the feasibility to construct an uneditable allele. Our study proposes an idea to narrow down the candidates of beneficial recoding sites. Meanwhile, we stress that the matched transcriptomes are needed to verify the conservation of editing events during evolution.https://www.tandfonline.com/doi/10.1080/19491034.2024.2304503A-to-I RNA editingAdarauto-recodingbeneficialeditablemetazoan |
| spellingShingle | Tianyou Zhao Ling Ma Shiwen Xu Wanzhi Cai Hu Li Yuange Duan Narrowing down the candidates of beneficial A-to-I RNA editing by comparing the recoding sites with uneditable counterparts Nucleus A-to-I RNA editing Adar auto-recoding beneficial editable metazoan |
| title | Narrowing down the candidates of beneficial A-to-I RNA editing by comparing the recoding sites with uneditable counterparts |
| title_full | Narrowing down the candidates of beneficial A-to-I RNA editing by comparing the recoding sites with uneditable counterparts |
| title_fullStr | Narrowing down the candidates of beneficial A-to-I RNA editing by comparing the recoding sites with uneditable counterparts |
| title_full_unstemmed | Narrowing down the candidates of beneficial A-to-I RNA editing by comparing the recoding sites with uneditable counterparts |
| title_short | Narrowing down the candidates of beneficial A-to-I RNA editing by comparing the recoding sites with uneditable counterparts |
| title_sort | narrowing down the candidates of beneficial a to i rna editing by comparing the recoding sites with uneditable counterparts |
| topic | A-to-I RNA editing Adar auto-recoding beneficial editable metazoan |
| url | https://www.tandfonline.com/doi/10.1080/19491034.2024.2304503 |
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