Mapping RNA-protein interactions with subcellular resolution using colocalization CLIP.
RNA
; 30(7): 920-937, 2024 Jun 17.
Article
em En
| MEDLINE
| ID: mdl-38658162
ABSTRACT
RNA-binding proteins (RBPs) are essential for RNA metabolism and profoundly impact health and disease. The subcellular organization of RBP interaction networks with target RNAs remains largely unexplored. Here, we develop colocalization CLIP (coCLIP), a method that combines cross-linking and immunoprecipitation (CLIP) with proximity labeling, to explore in-depth the subcellular RNA interactions of the RBP human antigen R (HuR). Using this method, we uncover HuR's dynamic and location-specific interactions with RNA, revealing alterations in sequence preferences and interactions in the nucleus, cytosol, or stress granule (SG) compartments. We uncover HuR's unique binding preferences within SGs during arsenite stress, illuminating intricate interactions that conventional methodologies cannot capture. Overall, coCLIP provides a powerful method for revealing RBP-RNA interactions based on localization and lays the foundation for an advanced understanding of RBP models that incorporate subcellular location as a critical determinant of their functions.
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Texto completo:
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Base de dados:
MEDLINE
Assunto principal:
Ligação Proteica
/
RNA
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Proteínas de Ligação a RNA
Limite:
Humans
Idioma:
En
Ano de publicação:
2024
Tipo de documento:
Article