Intron retention and its impact on gene expression and protein diversity: A review and a practical guide.
Wiley Interdiscip Rev RNA
; 12(1): e1631, 2021 01.
Article
en En
| MEDLINE
| ID: mdl-33073477
ABSTRACT
Intron retention (IR) occurs when a complete and unspliced intron remains in mature mRNA. An increasing body of literature has demonstrated a major role for IR in numerous biological functions, including several that impact human health and disease. Although experimental technologies used to study other forms of mRNA splicing can also be used to investigate IR, a specialized downstream computational analysis is optimal for IR discovery and analysis. Here we provide a review of IR and its biological implications, as well as a practical guide for how to detect and analyze it. Several methods, including long read third generation direct RNA sequencing, are described. We have developed an R package, FakIR, to facilitate the execution of the bioinformatic tasks recommended in this review and a tutorial on how to fit them to users aims. Additionally, we provide guidelines and experimental protocols to validate IR discovery and to evaluate the potential impact of IR on gene expression and protein output. This article is categorized under RNA Evolution and Genomics > Computational Analyses of RNA RNA Processing > Splicing Regulation/Alternative Splicing RNA Methods > RNA Analyses in vitro and In Silico.
Palabras clave
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Empalme del ARN
/
Empalme Alternativo
Tipo de estudio:
Guideline
Límite:
Humans
Idioma:
En
Revista:
Wiley Interdiscip Rev RNA
Año:
2021
Tipo del documento:
Article
País de afiliación:
Estados Unidos