Programming RNA Trans-Splicing for Versatile Gene Regulation and Complex Cellular Logic Computation

Synthetic biology aims to customize biological systems by programming genetic circuits. However, the scale and complexity of genetic circuits are limited by a shortage of composable, programmable, and orthogonal regulatory parts. Recently, split-intron-enabled trans-splicing riboregulators (SENTRs) have emerged as a promising tool for regulating gene expression at the post-transcriptional level, featuring low leakage expression, wide dynamic range (> 1000-fold), high predictability using machine learning, and orthogonality across multiple intronic components. SENTR's composability with other regulatory modalities, such as split inteins, enables the establishment of a novel split-biomolecule-enabled circuit design paradigm, unleashing the information-processing capacity of a single regulator gene for complex cellular logic computation with up to six inputs. Here, we describe the methods and strategies to implement SENTRs for efficient gene regulation, including computational design, experimental assessment, and statistical analysis of SENTR-based genetic circuits. Validated on ten genes encoding fluorescent proteins, transcription factors, and ncRNAs, this method can be readily utilized to develop SENTRs for diverse applications, such as stringent gene regulation, complex logic computation, and biosensing for intracellular RNAs or physiological biomarkers.