Multimodal control of Cas13 activity through domain insertion at an allosteric hotspot

CRISPR-Cas13 RNA nucleases have emerged as powerful tools for programmable RNA targeting. A light-controlled RNA nuclease could be transformative by enabling researchers to selectively knock down transcripts at desired positions in a cell or tissue or at timepoints of interest. Here, we develop a set of multimodal RfxCas13d tools that can be controlled by either light or small molecule addition. Screening an RfxCas13d library containing insertions of the AsLOV2 photoswitchable domain revealed an OptoCas13d-off variant that induced target RNA cleavage in the dark and switched to an inactive state under blue light. Insertion at this same allosteric hotspot could be further exploited to generate an OptoCas13d-on with the opposite light dependence and a ChemoCas13d that is activated upon the addition of rapamycin analogs. Through biochemical assays, we showed that AsLOV2 domain switching did not substantially affect Cas13d-RNA complex formation, indicating allosteric control over Cas13d catalytic activity. We applied the OptoCas13d-on system to target several endogenous transcripts and showed that it exhibited efficient mRNA knockdown only upon blue light illumination. Overall, our results demonstrate that engineered OptoCas13d can achieve cellular RNA modulation with high spatial and temporal precision.