A genetically encoded device for transcriptome storage in mammalian cells.

Abstract

Understanding how cells make decisions over time requires the ability to link past molecular states to future phenotypic outcomes. We present TimeVault, a genetically encoded system that records and stores transcriptomes within living mammalian cells for future readout. TimeVault leverages engineered vault particles that capture messenger RNA through polyadenosine [poly (A)]-binding protein. We demonstrate that the transcriptome stored by TimeVaults is stable in living cells for more than 7 days. TimeVault enables high-fidelity transcriptome-wide recording with minimal cellular perturbation, capturing transient stress responses and revealing gene expression changes underlying drug-naïve persister states in lung cancer cells that evade epidermal growth factor receptor (EGFR) inhibition. By linking past and present cellular states, TimeVault provides a powerful tool for decoding how cells respond to stress, make fate decisions, and resist therapy.