Emerging tools for exploring RNA regulation (LL4-3)

Abstract

RNA regulation is shifting to the forefront of gene expression in part because it has been difficult to study in the past; but new tools are making it more amenable to exploration on several levels from splicing to export to stability and translation. The field of RNA-protein interactions emerged with the cloning of cDNAs expressing RNA-binding proteins (RBPs) while the enzymes to synthesize cRNA and to map binding sites of RBPs with precision became available and provided important information related to RBP functions in splicing and translational control. In the early 1990s it was assumed that gene expression was solely coordinated at transcription, and that RNA-protein interactions were essentially single events. However, by using in vitro selection of naturally occurring sequences, it was demonstrated that RBPs could be multi-targeted on a larger scale to bind similar sequence elements in the 3′ UTRs of hundreds of brain-derived mRNAs. Later, microarrays allowed investigators to assess the steady-state levels of transcripts and were subsequently used to identify functionally related mRNAs associated with RBPs that govern their localization, coordination and dynamics. Many of the tools used in the discovery of coherent groups of mRNAs coordinated by RBPs in the immune system will be described. Moreover, the use of microarrays and next generation high-throughput sequencing procedures for detecting functional interactions of mRNAs and noncoding RNAs with regulatory RBPs on a genome-wide scale during immune responses will be presented.