Publications
RBPscan: A Quantitative, In Vivo Tool for Profiling RNA-Binding Protein Interactions
Abstract
RNA-binding proteins (RBPs) are essential regulators of gene expression at post-transcriptional 4 level, yet obtaining quantitative insights into RBP-RNA interactions in vivo remains a challenge. 5 Here we developed RBPscan, a method that integrates RNA editing with massively parallel 6 reporter assays (MPRAs) to profile RBP binding in vivo. RBPscan fuses the catalytic domain of 7 ADAR to the RBP of interest, using RNA editing of a recorder mRNA as a readout of binding 8 events. We demonstrate its utility in zebrafish embryos, human cells, and yeast, where it 9 quantifies binding strength, resolves dissociation constants, identifies high-specificity motifs for a 10 variety of RBPs, and links binding affinities to their impact on mRNA stability. RBPscan also 11 provides positional information of conserved and novel Pumilio-binding sites in lncRNA NORAD. 12 With its simplicity, scalability, and compatibility across systems, RBPscan offers a versatile tool 13 for investigating RBP-RNA interactions and complements established methods for studying post14 transcriptional regulatory networks.
Product Used
Variant Libraries
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