Constitutive patterns of gene expression regulated by RNA-binding proteins

Abstract

BackgroundRNA-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.ResultsWe 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.ConclusionsOur 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.

Advances in the characterization of RNA‐binding proteins

“…As observed for protein–protein interactions, structurally disordered regions bind with high specificity and low affinity . Hence, noncanonical domains, which are enriched in structural disorder, could promote low affinity interactions with RNA molecules . Accordingly, computational methods predict that the RNA‐binding ability of structural disorder is more pronounced in noncanonical RBPs, indicating that unfolded regions promote RNA interactions .…”

The cleverSuite approach for protein characterization: predictions of structural properties, solubility, chaperone requirements and RNA-binding abilities

“…Moreover, it has been observed that protein disorder is an important feature for RNA-binding proteins (Bellay et al , 2011; Cirillo et al , 2014). In agreement with this result, we found a significant enrichment in disorder propensities (Bhaskaran and Ponnuswamy, 1988; Campen et al , 2008).…”

A census of human RNA-binding proteins

“…Instead, the interactions of many RBPs in regulatory complexes determine specificity of PTGR processes. Hence, groups of RBPs in common PTGR pathways are often co-expressed and can drive coordinated expression of targets in cells and tissues, as well as across developmental processes 22,155,156 . Specific expression of RBPs can be used to deduce their putative roles and to identify novel components of regulatory pathways.…”