Anti-CRISPR RNAs: designing universal riboregulators with deep learning of Csy4-mediated RNA processing

RNA-based regulation offers a promising alternative of protein-based transcriptional networks. However, designing synthetic riboregulators with desirable functionalities using arbitrary sequences remains challenging, due in part to insufficient exploration of RNA sequence-to-function landscapes. Here we report that CRISPR-Csy4 mediates a nearly all-or-none processing of precursor CRISPR RNAs (pre-crRNAs), by profiling Csy4 binding sites flanked by > 1 million random sequences. This represents an ideal sequence-to-function space for universal riboregulator designs. Lacking discernible sequence-structural commonality among processable pre-crRNAs, we trained a neural network for accurate classification (f1-score {approx} 0.93). Inspired by exhaustive probing of palindromic flanking sequences, we designed anti-CRISPR RNAs (acrRNAs) that suppress processing of pre-crRNAs via stem stacking. We validated machine-learning-guided designs with >30 functional pairs of acrRNAs and pre-crRNAs to achieve switch-like properties. This opens a wide range of plug-and-play applications tailored through pre-crRNA designs, and represents a programmable alternative to protein-based anti-CRISPRs.