Sensitive monitoring of enhancer and noncoding RNA transcription via ribozyme-assisted RNA editing

The primary goal of this study is to provide tools for understanding transcriptional regulation of native genomic elements that combine high sensitivity, quantitative output, and broad applicability. Existing methods often have limited dynamic range, disrupt host RNAs, or fail to detect short-lived transcripts. Here, we present ribozyme-processed ADAR-engaging RNA-directed editing (REDDIT), a technology that converts transcriptional events into reporter protein translation via precise A-to-I RNA editing. REDDIT sensitively detects transcription from protein-coding genes, long noncoding RNAs (lncRNAs), primary microRNAs (pri-miRNAs), and enhancer RNAs (eRNAs), including low abundance and short-lived species, while minimally perturbing host gene expression, RNA processing, and the global editome. We apply REDDIT to monitor the naïve-to-primed transition in human embryonic stem cells (hESCs) and convert it into a transcription recorder that permanently logs transient and combinatorial transcriptional inputs when paired with Cre recombinase. Finally, by adapting REDDIT for high-throughput screening, we uncover multiple signaling pathways that regulate lncRNA and eRNA biogenesis. REDDIT therefore provides a scalable platform for quantitative monitoring and retrospective analysis of endogenous transcriptional dynamics across diverse genomic contexts.