Prediction of alternative pre-mRNA splicing outcomes.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
15 11 2023
15 11 2023
Historique:
received:
13
06
2023
accepted:
12
11
2023
medline:
17
11
2023
pubmed:
16
11
2023
entrez:
15
11
2023
Statut:
epublish
Résumé
To understand the biological impact of alternative pre-mRNA splicing, it is vital to know which exons are involved, what protein domains they encode, and how the translated isoforms differ. Therefore, we developed a computational pipeline (RiboSplitter) focused on functional effect prediction. It builds on event-based alternative splicing detection with additional filtering steps leading to more efficient statistical testing, and with detection of isoform-specific protein changes. A key methodological advance is reading frame prediction by translating exonic DNA in all possible frames, then finding a single open reading frame, or a single frame with matches to known proteins of the gene. This allowed unambiguous translation in 93.9% of alternative splicing events when tested on RNA-sequencing data of B cells from Sjögren's syndrome patients. RiboSplitter does not depend on reference annotations and translates events even when one or both isoform(s) are novel (unannotated). RiboSplitter's visualizations illustrate each event with translation outcomes, show event location within the gene, and align exons to protein domains.
Identifiants
pubmed: 37968320
doi: 10.1038/s41598-023-47348-6
pii: 10.1038/s41598-023-47348-6
pmc: PMC10651857
doi:
Substances chimiques
RNA Precursors
0
RNA, Messenger
0
Protein Isoforms
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
20000Informations de copyright
© 2023. The Author(s).
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