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

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.