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L-GIREMI uncovers RNA editing sites in long-read RNA-seq

Although long-read RNA-seq is increasingly applied to characterize full-length transcripts it can also enable detection of nucleotide variants, such as genetic mutations or RNA editing sites, which is significantly under-explored. Here, we present an in-depth study to detect and analyze RNA editing...

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Detalles Bibliográficos
Autores principales: Liu, Zhiheng, Quinones-Valdez, Giovanni, Fu, Ting, Huang, Elaine, Choudhury, Mudra, Reese, Fairlie, Mortazavi, Ali, Xiao, Xinshu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10360234/
https://www.ncbi.nlm.nih.gov/pubmed/37474948
http://dx.doi.org/10.1186/s13059-023-03012-w
Descripción
Sumario:Although long-read RNA-seq is increasingly applied to characterize full-length transcripts it can also enable detection of nucleotide variants, such as genetic mutations or RNA editing sites, which is significantly under-explored. Here, we present an in-depth study to detect and analyze RNA editing sites in long-read RNA-seq. Our new method, L-GIREMI, effectively handles sequencing errors and read biases. Applied to PacBio RNA-seq data, L-GIREMI affords a high accuracy in RNA editing identification. Additionally, our analysis uncovered novel insights about RNA editing occurrences in single molecules and double-stranded RNA structures. L-GIREMI provides a valuable means to study nucleotide variants in long-read RNA-seq. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-03012-w.