ARCHIVE: An Efficient Open-Ended DNA Recording Device Capable of Multiplex Capture of Pol-II Transcribed Signals

Engineering cell-based devices to record events into DNA has potential both as a non-ablative research tool and for enacting gene-circuit-based logic of cell therapies conditional on cell history. Whether as a means of understanding interactions on the single-cell level, or reconstructing histories of cellular events, a cellular DNA recording device has widespread utility, with prime editing-based methods at the forefront of this endeavor – notably peCHYRON. Open-ended recording tool resolution is inherently constrained by edit insertion efficiency however, and cannot yet capture RNA-polymerase II-transcribed signals, which constitute essentially all nuclear mammalian protein coding genes. To address this, we developed ARCHIVE (Amplified Recording of Cellular Histories into Information-dense Vectors of Events) by using machine-learning assisted prediction of prime-editing efficiency as a surrogate fitness model for generative in silico pegRNA evolution. ARCHIVE is a recording module capable of integrating RNA-encoded signals into predefined genomic loci with unprecedented efficiency and an order-of-magnitude improvement in temporal resolution.