Scott Tenenbaum, SUNY- Polytechnic Institute, Albany

sxRNA: A Trans-Regulated, miRNA Activated, Switch Technology

 

Francis Doyle, Zachary E. Wurz and Scott A. Tenenbaum*

 

Colleges of Nanoscale Science and Engineering, Nanobioscience Constellation, SUNY-Polytechnic Institute, Albany, New York 12203, USA

 

The wide array of vital functions that RNA performs is dependent on its ability to dynamically fold into alternative structures in response to changes in intracellular and extracellular conditions. RNA-binding proteins (RBPs) regulate much of this activity by targeting specific RNA structures or motifs. RNA three-way junctions (3WJs) are naturally occurring structural elements found in many functional RNA molecules, such as ribosomal RNA and ribozymes. These structures are classically characterized as resulting from an RNA molecule folding back on itself in cis to produce three separate helices that meet around a central unpaired region. However, 3WJs can also be formed in trans when a non-coding RNA binds to a messenger RNA target. 3WJs created in trans can be viewed as a new category of regulatory RNA that we have called structurally interacting RNA or “sxRNA” for short that relies on the unique expression of a targeted microRNA of interest to control the expression of an ectopic gene of interest. By coupling post-transcriptional gene regulation with the unique microRNA signature patterns in cell types, sxRNA technology can enable the cell specific expression of a desired protein or reporter gene to positively or negatively select for a tissue type, disease process or developmental stage. We design sxRNAs in which the natural RBP-motif is altered so it only correctly forms when a targeted “trigger” miRNA, binds in trans and stabilizes it by base-pairing to the flanking region restoring a functional motif. When tethered downstream of a coding reporter mRNA, sxRNA can be act as a translational switch with reporter production dependent on amount of the trigger miRNA.