Mapping transcriptome-wide protein-RNA interactions to elucidate RNA regulatory programs

Abstract

Background: Our understanding of post-transcriptional gene regulation has increased exponentially with the development of robust methods to define protein-RNA interactions across the transcriptome. In this review, we highlight the evolution and successful applications of crosslinking and immunoprecipitation (CLIP) methods to interrogate protein-RNA interactions in a transcriptome-wide manner.

Results: Here, we survey the vast array of in vitro and in vivo approaches used to identify protein-RNA interactions, including but not limited to electrophoretic mobility shift assays, systematic evolution of ligands by exponential enrichment (SELEX), and RIP-seq. We particularly emphasize the advancement of CLIP technologies, and detail protocol improvements and computational tools used to analyze the output data. Importantly, we discuss how profiling protein-RNA interactions can delineate biological functions including splicing regulation, alternative polyadenylation, cytoplasmic decay substrates, and miRNA targets.

Conclusions: In summary, this review summarizes the benefits of characterizing RNA-protein networks to further understand the regulation of gene expression and disease pathogenesis. Our review comments on how future CLIP technologies can be adapted to address outstanding questions related to many aspects of RNA metabolism and further advance our understanding of RNA biology.

Graphical abstract

Keywords

RNA binding proteins / CLIP / post-transcriptional regulation / RNA networks

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ACKNOWLEDGEMENTS

This work was supported by funds from the National Institutes of Health to LLZ (T32 GM08056) and DDL (R01 GM107331), USA.

COMPLIANCE WITH ETHICS GUIDELINES

The authors Molly M. Hannigan, Leah L. Zagore and Donny D. Licatalosi declare that they have no conflict of interests.

This article is a review article and does not contain any studies with human or animal subjects performed by any of the authors.

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