L-GIREMI uncovers RNA editing sites in long-read RNA-seq.
A-to-I editing
Double-stranded RNA
Mutual information
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
20 07 2023
20 07 2023
Historique:
received:
22
03
2022
accepted:
12
07
2023
medline:
24
7
2023
pubmed:
21
7
2023
entrez:
20
7
2023
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 37474948
doi: 10.1186/s13059-023-03012-w
pii: 10.1186/s13059-023-03012-w
pmc: PMC10360234
doi:
Substances chimiques
Nucleotides
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
171Subventions
Organisme : NCI NIH HHS
ID : R01 CA262686
Pays : United States
Organisme : NIMH NIH HHS
ID : R01 MH123177
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG009417
Pays : United States
Organisme : NHGRI NIH HHS
ID : UM1 HG009443
Pays : United States
Informations de copyright
© 2023. The Author(s).
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