Small Molecule-Inducible RNA-Targeting Systems for Temporal Control of RNA Regulation

All aspects of mRNA lifetime and function, including its stability, translational to protein, and trafficking through the cell, are tightly regulated through coordinated post-transcriptional modifications and interactions with a multitude of effector proteins. Despite the increasing recognition of RNA regulation as a critical layer of mammalian gene expression control and its increasing excitement as a therapeutic target, tools to study and control RNA regulatory mechanisms with temporal precision in their endogenous environment are lacking. Here, we present small molecule-inducible RNA-targeting effectors based on our previously-developed CRISPR/Cas-inspired RNA targeting system (CIRTS). The CIRTS biosensor system is based on guide RNA (gRNA)-dependent RNA binding domains that interact with a target transcript using Watson-Crick-Franklin base pair interactions. Addition of a small molecule recruits an RNA effector to the target transcript, thereby eliciting a local effect on the transcript. In this work, we showcase that these CIRTS biosensors can trigger inducible RNA editing, degradation, or translation on target transcripts in a small molecule-dependent manner. We further go on to show that the new CIRTS editor can induce RNA base editing in a small molecule-dependent manner in vivo. Collectively this work provides a useful new set of tools to probe the dynamics of RNA regulatory systems and a new approach to control gene expression at the RNA level.