Identification of Novel Proteins Binding the AU-rich Element of α-prothymosin MRNA Through the Selection of Open Reading Frames (RIDome)

Overview

Journal RNA Biol

Specialty Molecular Biology

Date 2015 Oct 30

PMID 26512911

Citations 4

Authors

Laura Patrucco

Clelia Peano

Andrea Chiesa

Filomena Guida

Imma Luisi

Ilenia Boria

Flavio Mignone

Gianluca De Bellis

Silvia Zucchelli

Stefano Gustincich

Claudio Santoro

Daniele Sblattero

Diego Cotella

Affiliations

Soon will be listed here.

Abstract

We describe here a platform for high-throughput protein expression and interaction analysis aimed at identifying the RNA-interacting domainome. This approach combines the selection of a phage library displaying "filtered" open reading frames with next-generation DNA sequencing. The method was validated using an RNA bait corresponding to the AU-rich element of α-prothymosin, an RNA motif that promotes mRNA stability and translation through its interaction with the RNA-binding protein ELAVL1. With this strategy, we not only confirmed known RNA-binding proteins that specifically interact with the target RNA (such as ELAVL1/HuR and RBM38) but also identified proteins not previously known to be ARE-binding (R3HDM2 and RALY). We propose this technology as a novel approach for studying the RNA-binding proteome.

Citing Articles

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Espinoza S, Bon C, Valentini P, Pierattini B, Matey A, Damiani D Essays Biochem. 2021; 65(4):775-789.

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InteractomeSeq: a web server for the identification and profiling of domains and epitopes from phage display and next generation sequencing data.

Puccio S, Grillo G, Consiglio A, Soluri M, Sblattero D, Cotella D Nucleic Acids Res. 2020; 48(W1):W200-W207.

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The RNA-binding protein ILF3 binds to transposable element sequences in SINEUP lncRNAs.

Fasolo F, Patrucco L, Volpe M, Bon C, Peano C, Mignone F FASEB J. 2019; 33(12):13572-13589.

PMID: 31570000 PMC: 6894054. DOI: 10.1096/fj.201901618RR.

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing.

Soluri M, Puccio S, Caredda G, Grillo G, Licciulli V, Consiglio A J Vis Exp. 2018; (140).

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