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PRIMA: a gene-centered, RNA-to-protein method for mapping RNA-protein interactions

Authors :
Albertha J.M. Walhout
Alex M. Tamburino
Ebru Kaymak
Shaleen Shrestha
Amy D. Holdorf
Sean P. Ryder
Publication Year :
2016
Publisher :
Cold Spring Harbor Laboratory, 2016.

Abstract

SUMMARYInteractions between RNA binding protein (RBP) and mRNAs are critical to post-transcriptional gene regulation. Eukaryotic genomes encode thousands of mRNAs and hundreds of RBPs. However, in contrast to interactions between transcription factors (TFs) and DNA, the interactome between RBPs and RNA has been explored for only a small number of proteins and RNAs. This is largely because the focus has been on using ‘protein-centered’ (RBP-to-RNA) interaction mapping methods that identify the RNAs with which an individual RBP interacts. While powerful, these methods cannot as of yet be applied to the entire RBPome. Moreover, it may be desirable for a researcher to identify the repertoire of RBPs that can interact with an mRNA of interest – in a ‘gene-centered’ manner, yet few such techniques are available. Here, we present Protein-RNA Interaction Mapping Assay (PRIMA) with which an RNA ‘bait’ can be tested versus multiple RBP ‘preys’ in a single experiment. PRIMA is a translation-based assay that examines interactions in the yeast cytoplasm, the cellular location of mRNA translation. We show that PRIMA can be used with small RNA elements, as well as with full-lengthCaenorhabditis elegans3′UTRs. PRIMA faithfully recapitulates numerous well-characterized RNA-RBP interactions and also identified novel interactions, some of which were confirmedin vivo. We envision that PRIMA will provide a complementary tool to expand the depth and scale with which the RNA-RBP interactome can be explored.

Details

Language :
English
Database :
OpenAIRE
Accession number :
edsair.doi.dedup.....b1cc77d7eb4d4226b498e1a6bf396ab6
Full Text :
https://doi.org/10.1101/074823