Identification and Interpretation of A-to-I RNA Editing Events in Insect Transcriptomes
Adenosine-to-inosine (A-to-I) RNA editing is the most prevalent RNA modification in the nervous systems of metazoans. To study the biological significance of RNA editing, we first have to accurately identify these editing events from the transcriptome. The genome-wide identification of RNA editing s...
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MDPI AG
2023-12-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/24/17126 |
| _version_ | 1797380781795966976 |
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| author | Ye Xu Jiyao Liu Tianyou Zhao Fan Song Li Tian Wanzhi Cai Hu Li Yuange Duan |
| author_facet | Ye Xu Jiyao Liu Tianyou Zhao Fan Song Li Tian Wanzhi Cai Hu Li Yuange Duan |
| author_sort | Ye Xu |
| collection | DOAJ |
| description | Adenosine-to-inosine (A-to-I) RNA editing is the most prevalent RNA modification in the nervous systems of metazoans. To study the biological significance of RNA editing, we first have to accurately identify these editing events from the transcriptome. The genome-wide identification of RNA editing sites remains a challenging task. In this review, we will first introduce the occurrence, regulation, and importance of A-to-I RNA editing and then describe the established bioinformatic procedures and difficulties in the accurate identification of these sit esespecially in small sized non-model insects. In brief, (1) to obtain an accurate profile of RNA editing sites, a transcriptome coupled with the DNA resequencing of a matched sample is favorable; (2) the single-cell sequencing technique is ready to be applied to RNA editing studies, but there are a few limitations to overcome; (3) during mapping and variant calling steps, various issues, like mapping and base quality, soft-clipping, and the positions of mismatches on reads, should be carefully considered; (4) Sanger sequencing of both RNA and the matched DNA is the best verification of RNA editing sites, but other auxiliary evidence, like the nonsynonymous-to-synonymous ratio or the linkage information, is also helpful for judging the reliability of editing sites. We have systematically reviewed the understanding of the biological significance of RNA editing and summarized the methodology for identifying such editing events. We also raised several promising aspects and challenges in this field. With insightful perspectives on both scientific and technical issues, our review will benefit the researchers in the broader RNA editing community. |
| first_indexed | 2024-03-08T20:42:58Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-08T20:42:58Z |
| publishDate | 2023-12-01 |
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| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-a22897e5188c4327b8bd9f03afa334fc2023-12-22T14:13:19ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-12-0124241712610.3390/ijms242417126Identification and Interpretation of A-to-I RNA Editing Events in Insect TranscriptomesYe Xu0Jiyao Liu1Tianyou Zhao2Fan Song3Li Tian4Wanzhi Cai5Hu Li6Yuange Duan7MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, ChinaMOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, ChinaMOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, ChinaMOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, ChinaMOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, ChinaMOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, ChinaMOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, ChinaMOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, ChinaAdenosine-to-inosine (A-to-I) RNA editing is the most prevalent RNA modification in the nervous systems of metazoans. To study the biological significance of RNA editing, we first have to accurately identify these editing events from the transcriptome. The genome-wide identification of RNA editing sites remains a challenging task. In this review, we will first introduce the occurrence, regulation, and importance of A-to-I RNA editing and then describe the established bioinformatic procedures and difficulties in the accurate identification of these sit esespecially in small sized non-model insects. In brief, (1) to obtain an accurate profile of RNA editing sites, a transcriptome coupled with the DNA resequencing of a matched sample is favorable; (2) the single-cell sequencing technique is ready to be applied to RNA editing studies, but there are a few limitations to overcome; (3) during mapping and variant calling steps, various issues, like mapping and base quality, soft-clipping, and the positions of mismatches on reads, should be carefully considered; (4) Sanger sequencing of both RNA and the matched DNA is the best verification of RNA editing sites, but other auxiliary evidence, like the nonsynonymous-to-synonymous ratio or the linkage information, is also helpful for judging the reliability of editing sites. We have systematically reviewed the understanding of the biological significance of RNA editing and summarized the methodology for identifying such editing events. We also raised several promising aspects and challenges in this field. With insightful perspectives on both scientific and technical issues, our review will benefit the researchers in the broader RNA editing community.https://www.mdpi.com/1422-0067/24/24/17126A-to-I RNA editingidentificationmethodology |
| spellingShingle | Ye Xu Jiyao Liu Tianyou Zhao Fan Song Li Tian Wanzhi Cai Hu Li Yuange Duan Identification and Interpretation of A-to-I RNA Editing Events in Insect Transcriptomes International Journal of Molecular Sciences A-to-I RNA editing identification methodology |
| title | Identification and Interpretation of A-to-I RNA Editing Events in Insect Transcriptomes |
| title_full | Identification and Interpretation of A-to-I RNA Editing Events in Insect Transcriptomes |
| title_fullStr | Identification and Interpretation of A-to-I RNA Editing Events in Insect Transcriptomes |
| title_full_unstemmed | Identification and Interpretation of A-to-I RNA Editing Events in Insect Transcriptomes |
| title_short | Identification and Interpretation of A-to-I RNA Editing Events in Insect Transcriptomes |
| title_sort | identification and interpretation of a to i rna editing events in insect transcriptomes |
| topic | A-to-I RNA editing identification methodology |
| url | https://www.mdpi.com/1422-0067/24/24/17126 |
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