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Open Access Highly Accessed Research

Constitutive patterns of gene expression regulated by RNA-binding proteins

Davide Cirillo12, Domenica Marchese12, Federico Agostini12, Carmen Maria Livi12, Teresa Botta-Orfila12 and Gian Gaetano Tartaglia12*

Author Affiliations

1 Gene Function and Evolution, Centre for Genomic Regulation (CRG), Dr Aiguader 88, Barcelona 08003, Spain

2 Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain

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Genome Biology 2014, 15:R13  doi:10.1186/gb-2014-15-1-r13

Published: 9 January 2014

Abstract

Background

RNA-binding proteins regulate a number of cellular processes, including synthesis, folding, translocation, assembly and clearance of RNAs. Recent studies have reported that an unexpectedly large number of proteins are able to interact with RNA, but the partners of many RNA-binding proteins are still uncharacterized.

Results

We combined prediction of ribonucleoprotein interactions, based on catRAPID calculations, with analysis of protein and RNA expression profiles from human tissues. We found strong interaction propensities for both positively and negatively correlated expression patterns. Our integration of in silico and ex vivo data unraveled two major types of protein–RNA interactions, with positively correlated patterns related to cell cycle control and negatively correlated patterns related to survival, growth and differentiation. To facilitate the investigation of protein–RNA interactions and expression networks, we developed the catRAPID express web server.

Conclusions

Our analysis sheds light on the role of RNA-binding proteins in regulating proliferation and differentiation processes, and we provide a data exploration tool to aid future experimental studies.