Modeling Dynamic Transcriptional Circuits with CRISPRi

Abstract

Targeted transcriptional repression with catalytically inactive Cas9 (CRISPRi) can be used to build gene regulatory nets similar in principle to those made with traditional transcription factors, and promises to do so with better orthogonality, programmability, and extensibility. We use a simple dynamical model of CRISPRi to understand its behavior and requirements, and to show that CRISPRi can recapitulate several classic gene regulatory circuits, including the repressilator, a toggle switch, and an incoherent feed-forward loop pulse generator. Our model also predicts that these circuits are highly sensitive to promoter leak, but that promoter leak can be offset with active degradation of dCas. We provide specifications for required fold-repression and dCas degradation rates for several dynamic circuits. Our modeling reveals key engineering requirements and considerations for the construction of dynamic CRISPRi circuits, and provides a roadmap for building those circuits.