Advances in the characterization of RNA‐binding proteins

Abstract

From transcription, to transport, storage, and translation, RNA depends on association with different RNA‐binding proteins (RBPs). Methods based on next‐generation sequencing and protein mass‐spectrometry have started to unveil genome‐wide interactions of RBPs but many aspects still remain out of sight. How many of the binding sites identified in high‐throughput screenings are functional? A number of computational methods have been developed to analyze experimental data and to obtain insights into the specificity of protein–RNA interactions. How can theoretical models be exploited to identify RBPs? In addition to oligomeric complexes, protein and RNA molecules can associate into granular assemblies whose physical properties are still poorly understood. What protein features promote granule formation and what effects do these assemblies have on cell function? Here, we describe the newest in silico, in vitro, and in vivo advances in the field of protein–RNA interactions. We also present the challenges that experimental and computational approaches will have to face in future studies. WIREs RNA 2016, 7:793–810. doi: 10.1002/wrna.1378For further resources related to this article, please visit the WIREs website.

A Comprehensive Analysis of RALF Proteins in Green Plants Suggests There Are Two Distinct Functional Groups

“…CleverMachine (Klus et al, 2014) allows for the detection of protein properties that differ between two datasets and has been used to distinguish P-bodies and stress granules from other globular proteins (Marchese et al, 2016) and to classify homo-repeat proteins (Yu Lobanov et al, 2016). A multi-cleverMachine property prediction and comparison of the RALFs reveals that the clade IV proteins differ in a variety of physico-chemical properties from the other clades (Figure S4), such as a reduced disorder propensity.…”

Denaturing CLIP, dCLIP, Pipeline Identifies Discrete RNA Footprints on Chromatin-Associated Proteins and Reveals that CBX7 Targets 3′ UTRs to Regulate mRNA Expression

“…While current methodologies have been excellent for highly abundant proteins, including cytoplasmic RNA-binding proteins (Marchese et al, 2016), nuclear epigenetic complexes have presented a greater challenge because of their chromatin association and (hence) a less soluble nature, Such proteins also tend to exist in multi-subunit complexes, with the potential to have several points of contact within a long transcript. New, highly stringent methods that complement existing techniques are therefore much needed in order to obtain a well-rounded view of specific RNA-protein networks.…”

Partner‐specific prediction of RNA‐binding residues in proteins: A critical assessment

“…This finding, together with the availability of increasing number of computational tools for predicting IDRs from protein sequence, suggests a promising direction for developing improved protein‐RNA binding site prediction models that incorporate information derived from IDRs. Another promising direction is to leverage high throughput data from protein‐RNA binding assays and affinity distributions, to generate the RNA binding models for RBPs . It should also be possible to incorporate a more nuanced notion of RNA partner‐specificity into the training of RNA‐binding residues in RBPs.…”

“…The large numbers of proteins and RNAs in living cells constitute complex networks of RNA‐protein interactions . There is growing evidence that aberrations or dysregulation of the expression of RNA‐binding proteins (RBPs) are associated with diseases, including neurodegeneration and cancer . Hence, deciphering the RNA‐protein recognition code is important for understanding the sequence and structural determinants of the specificity and affinity of RNA binding sites of RBPs, which is essential both for comprehending the functional implications of protein‐RNA interactions and for developing new therapeutic strategies for many diseases.…”