Computational design of small transcription activating RNAs for versatile and dynamic gene regulation

TLDR

Synthetic biology seeks programmable control of cellular functions, and RNA regulators enable bottom‑up design of versatile, programmable gene‑expression systems. The study introduces a computational design method to generate bacterial Small Transcription Activating RNAs (STARs) that can achieve up to ~9000‑fold gene activation. The authors computationally design STARs, build a library of orthogonal variants, and integrate them with each other and CRISPRi repressors to construct RNA‑based circuits enabling sophisticated temporal control. STARs synergize with existing regulators, reprogram cellular phenotypes, control multigene pathways, and, when combined with CRISPRi, enable sophisticated temporal gene‑expression circuits.

Abstract

Abstract A longstanding goal of synthetic biology has been the programmable control of cellular functions. Central to this is the creation of versatile regulatory toolsets that allow for programmable control of gene expression. Of the many regulatory molecules available, RNA regulators offer the intriguing possibility of de novo design—allowing for the bottom-up molecular-level design of genetic control systems. Here we present a computational design approach for the creation of a bacterial regulator called Small Transcription Activating RNAs (STARs) and create a library of high-performing and orthogonal STARs that achieve up to ~ 9000-fold gene activation. We demonstrate the versatility of these STARs—from acting synergistically with existing constitutive and inducible regulators, to reprogramming cellular phenotypes and controlling multigene metabolic pathway expression. Finally, we combine these new STARs with themselves and CRISPRi transcriptional repressors to deliver new types of RNA-based genetic circuitry that allow for sophisticated and temporal control of gene expression.