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

作者：Longxian Chen, Liang Ou, Xinyun Jing, Yimeng Kong, Bingran Xie, Niubing Zhang, Hanping Shi, Hang Qin, Xuan Li, Pei Hao · 发表于：Genome biology · 年份：2023 · DOI：10.1186/s13059-023-02921-0 · 被引用次数：41 · 研究领域：RNA regulation and disease、RNA and protein synthesis mechanisms、RNA Research and Splicing

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.