Programmable RNA Sensing for Cell Monitoring and Manipulation

RNAs are the central and universal mediator of genetic information underlying the diversity of cell types and cell states, which together shape tissue organization and organismal function across species and life spans. Despite advances in RNA sequencing and massive accumulation of transcriptome datasets across life sciences, the dearth of technologies that leverage RNAs to observe and manipulate cell types remains a prohibitive bottleneck in biology and medicine. Here, we describe CellREADR (Cell access through RNA sensing by Endogenous ADAR), a programmable RNA sensing technology that leverages RNA editing mediated by ADAR (adenosine deaminase acting on RNA) for coupling the detection of cell-defining RNAs with translation of effector proteins. Viral delivery of CellREADR conferred specific cell type access in mouse and rat brains and in ex vivo human brain tissues. Furthermore, CellREADR enabled recording and control of neuron types in behaving mice. CellREADR thus highlights the potential for RNA-based monitoring and editing of animal cells in ways that are specific, versatile, easy, and generalizable across organ systems and species, with broad applications in biology, biotechnology, and programmable RNA medicine.