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Updated: Feb 15, 2026

Novel RNA-Binding Proteins Isolation by the RaPID Methodology
Published on: September 30, 2016
PTRE-seq reveals mechanism and interactions of RNA binding proteins and miRNAs
Kyle A Cottrell1, Hemangi G Chaudhari2,3, Barak A Cohen2,3
1Department of Cell Biology and Physiology, School of Medicine, Washington University, St. Louis, MO, 63110, USA.
Abstract:
RNA binding proteins (RBP) and microRNAs (miRNAs) often bind sequences in 3' untranslated regions (UTRs) of mRNAs, and regulate stability and translation efficiency. With the identification of numerous RBPs and miRNAs, there is an urgent need for new technologies to dissect the function of the cis-acting elements of RBPs and miRNAs. We describe post-transcriptional regulatory element sequencing (PTRE-seq), a massively parallel method for assaying the target sequences of miRNAs and RBPs. We use PTRE-seq to dissect sequence preferences and interactions between miRNAs and RBPs. The binding sites for these effector molecules influenced different aspects of the RNA lifecycle: RNA stability, translation efficiency, and translation initiation. In some cases, post-transcriptional control is modular, with different factors acting independently of each other, while in other cases factors show specific epistatic interactions. The throughput, flexibility, and reproducibility of PTRE-seq make it a valuable tool to study post-transcriptional regulation by 3'UTR elements.
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