Identification of CELF1 RNA targets by CLIP-seq in human HeLa cells

Olivier Le Tonquèze,Bernhard Gschloessl,Vincent Legagneux,Luc Paillard,Yann Audic

doi:10.1016/j.gdata.2016.04.009

Abstract

The specific interactions between RNA-binding proteins and their target RNAs are an essential level to control gene expression. By combining ultra-violet cross-linking and immunoprecipitation (CLIP) and massive SoliD sequencing we identified the RNAs bound by the RNA-binding protein CELF1, in human HeLa cells. The CELF1 binding sites deduced from the sequence data allow characterizing specific features of CELF1-RNA association. We present therefore the first map of CELF1 binding sites in human cells.

Highlights

Regulatory RNA binding proteins play a role in the processing of the RNA molecules by controlling the many steps that follow transcription
This reveals that only RNAs associated with CELF1 can be retrieved from cross-linking and immunoprecipitation (CLIP) experiments run in these cells
The cell extracts were treated with RNAse T1 to generate small ribonucleic complexes (Fig. 1B(a)) that were immunoprecipitated using magnetic beads coupled to anti-CELF1 antibody

Summary

Introduction

Regulatory RNA binding proteins play a role in the processing of the RNA molecules by controlling the many steps that follow transcription This includes but is not limited to nuclear splicing, cleavage and polyadenylation, nuclear export and cytoplasmic localization of the mRNA, cytoplasmic deadenylation, RNA degradation and translational control of messenger RNA. CELF1 (CUGBP, Elav-like family member 1, named CUGBP1) is a conserved RNA binding protein that controls alternative splicing in the nucleus and cytoplasmic deadenylation, mRNA stability and translation in the cytoplasm [5]. It has been implicated in several pathological conditions.

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Conclusion