TimeVault turns vault particles into molecular memory of transcriptional states: how to decode the cellular black box.

Abstract

Cellular phenotypes are shaped not only by current molecular states but by transient transcriptional programs that encode prior experiences and influence future behavior. Conventional transcriptomic approaches, including bulk and single-cell RNA sequencing, provide high-resolution snapshots of gene expression but are intrinsically destructive, precluding direct linkage between past transcriptional states and downstream cellular fate. In this context, "TimeVault" introduces a fundamentally new paradigm by enabling intracellular storage of endogenous transcriptomes within living cells. By repurposing vault ribonucleoprotein particles to sequester and stabilize polyadenylated mRNA, TimeVault preserves unbiased, transcriptome-wide records of transcriptional states over timescales far exceeding native mRNA half-lives. This capability allows retrospective reconstruction of molecular histories that would otherwise be lost, bridging a critical gap between transient gene expression and long-term phenotypic outcomes. Application of TimeVault to canonical stress responses demonstrates precise temporal gating and durable transcript preservation, while its use in cancer models reveals preexisting transcriptional programs that predict drug-tolerant persister cell formation prior to therapy. These findings highlight the power of molecular memory devices to uncover causal relationships that remain invisible to conventional endpoint analyses. TimeVault establishes intracellular transcriptome archiving as a versatile tool with broad implications for developmental biology, stress adaptation, and therapeutic resistance.