RNA-centric approaches to study RNA-protein interactions in vitro and in silico.
Methods
; 178: 11-18, 2020 06 01.
Article
em En
| MEDLINE
| ID: mdl-31563541
ABSTRACT
Given their central role in translation, splicing, localization and stability of transcripts, RNA binding proteins (RBPs) are key regulators of several cellular processes. While experimental efforts have been put to study how RBPs bind to transcripts, very little is known about the RNA contributions to the interaction. Here, we review the most common RNA-centric methods to reveal interactions with RBPs both in vitro (SELEX, SEQR, RNA-compete and RBNS) and in silico (MEME, SeAMotE, GLAM2, iDeep, MEMERIS, RNA context, RCK, RNApromo and GraphProt). We emphasize the main advantages and disadvantages of each technique and highlight the key physico-chemical features contributing to the identification of RNA motifs involved in RBP recognition. We discuss extrinsic determinants influencing protein-RNA binding, such as post-transcriptional and post-translational modifications as well as expression and location of transcripts.
Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
RNA
/
Proteínas de Ligação a RNA
/
Conformação de Ácido Nucleico
Tipo de estudo:
Prognostic_studies
Idioma:
En
Ano de publicação:
2020
Tipo de documento:
Article