Advances in endogenous RNA pull-down: A straightforward dextran sulfate-based method enhancing RNA recovery

Abstract

Detecting RNA/RNA interactions in the context of a given cellular system is crucial to gain insights into the molecular mechanisms that stand beneath each specific RNA molecule. When it comes to non-protein coding RNA (ncRNAs), and especially to long noncoding RNAs (lncRNAs), the reliability of the RNA purification is dramatically dependent on their abundance. Exogenous methods, in which lncRNAs are in vitro transcribed and incubated with protein extracts or overexpressed by cell transfection, have been extensively used to overcome the problem of abundance. However, although useful to study the contribution of single RNA sub-modules to RNA/protein interactions, these exogenous practices might fail in revealing biologically meaningful contacts occurring in vivo and risk to generate non-physiological artifacts. Therefore, endogenous methods must be preferred, especially for the initial identification of partners specifically interacting with elected RNAs. Here, we apply an endogenous RNA pull-down to lncMN2-203, a neuron-specific lncRNA contributing to the robustness of motor neurons specification, through the interaction with miRNA-466i-5p. We show that both the yield of lncMN2-203 recovery and the specificity of its interaction with the miRNA dramatically increase in the presence of Dextran Sulfate Sodium (DSS) salt. This new set-up may represent a powerful means for improving the study of RNA-RNA interactions of biological significance, especially for those lncRNAs whose role as microRNA (miRNA) sponges or regulators of mRNA stability was demonstrated.

Exploring the landscape of tools and resources for the analysis of long non-coding RNAs

“…In fact, the advance of in silico tools, that are thought for their direct and immediate application, is accompanied by the need of new structural, molecular and biochemical bench-based approaches. These can be either RNA or protein-centric methods for the analysis of RNA-protein interactions [130] , or refined with the use of psoralen or dextran sulfate for improving the study of RNA-RNA interactions [131] , [132] . These biochemical approaches are increasing the stringency and the accuracy to assess in vivo the predictions obtained using bioinformatics pipelines.…”