DeepEdit: single-molecule detection and phasing of A-to-I RNA editing events using nanopore direct RNA sequencing

Single-molecule detection and phasing of A-to-I RNA editing events remain an unresolved problem. Long-read and PCR-free nanopore native RNA sequencing offers a great opportunity for direct RNA editing detection. Here, we develop a neural network model, DeepEdit, that not only recognizes A-to-I editi...

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Autores principales: Chen, Longxian, Ou, Liang, Jing, Xinyun, Kong, Yimeng, Xie, Bingran, Zhang, Niubing, Shi, Han, Qin, Hang, Li, Xuan, Hao, Pei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Short Report
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10108526/
https://www.ncbi.nlm.nih.gov/pubmed/37069604
http://dx.doi.org/10.1186/s13059-023-02921-0
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author Chen, Longxian
Ou, Liang
Jing, Xinyun
Kong, Yimeng
Xie, Bingran
Zhang, Niubing
Shi, Han
Qin, Hang
Li, Xuan
Hao, Pei
author_facet Chen, Longxian
Ou, Liang
Jing, Xinyun
Kong, Yimeng
Xie, Bingran
Zhang, Niubing
Shi, Han
Qin, Hang
Li, Xuan
Hao, Pei
author_sort Chen, Longxian
collection PubMed
description Single-molecule detection and phasing of A-to-I RNA editing events remain an unresolved problem. Long-read and PCR-free nanopore native RNA sequencing offers a great opportunity for direct RNA editing detection. Here, we develop a neural network model, DeepEdit, that not only recognizes A-to-I editing events in single reads of Oxford Nanopore direct RNA sequencing, but also resolves the phasing of RNA editing events on transcripts. We illustrate the robustness of DeepEdit by applying it to Schizosaccharomyces pombe and Homo sapiens transcriptome data. We anticipate DeepEdit to be a powerful tool for the study of RNA editing from a new perspective. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-02921-0.
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spelling pubmed-101085262023-04-18 DeepEdit: single-molecule detection and phasing of A-to-I RNA editing events using nanopore direct RNA sequencing Chen, Longxian Ou, Liang Jing, Xinyun Kong, Yimeng Xie, Bingran Zhang, Niubing Shi, Han Qin, Hang Li, Xuan Hao, Pei Genome Biol Short Report Single-molecule detection and phasing of A-to-I RNA editing events remain an unresolved problem. Long-read and PCR-free nanopore native RNA sequencing offers a great opportunity for direct RNA editing detection. Here, we develop a neural network model, DeepEdit, that not only recognizes A-to-I editing events in single reads of Oxford Nanopore direct RNA sequencing, but also resolves the phasing of RNA editing events on transcripts. We illustrate the robustness of DeepEdit by applying it to Schizosaccharomyces pombe and Homo sapiens transcriptome data. We anticipate DeepEdit to be a powerful tool for the study of RNA editing from a new perspective. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-02921-0. BioMed Central 2023-04-17 /pmc/articles/PMC10108526/ /pubmed/37069604 http://dx.doi.org/10.1186/s13059-023-02921-0 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Short Report
Chen, Longxian
Ou, Liang
Jing, Xinyun
Kong, Yimeng
Xie, Bingran
Zhang, Niubing
Shi, Han
Qin, Hang
Li, Xuan
Hao, Pei
DeepEdit: single-molecule detection and phasing of A-to-I RNA editing events using nanopore direct RNA sequencing
title DeepEdit: single-molecule detection and phasing of A-to-I RNA editing events using nanopore direct RNA sequencing
title_full DeepEdit: single-molecule detection and phasing of A-to-I RNA editing events using nanopore direct RNA sequencing
title_fullStr DeepEdit: single-molecule detection and phasing of A-to-I RNA editing events using nanopore direct RNA sequencing
title_full_unstemmed DeepEdit: single-molecule detection and phasing of A-to-I RNA editing events using nanopore direct RNA sequencing
title_short DeepEdit: single-molecule detection and phasing of A-to-I RNA editing events using nanopore direct RNA sequencing
title_sort deepedit: single-molecule detection and phasing of a-to-i rna editing events using nanopore direct rna sequencing
topic Short Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10108526/
https://www.ncbi.nlm.nih.gov/pubmed/37069604
http://dx.doi.org/10.1186/s13059-023-02921-0
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