PT  - JOURNAL ARTICLE
AU  - Santi Bhattarai-Kline
AU  - Elana Lockshin
AU  - Max G. Schubert
AU  - Jeff Nivala
AU  - George Church
AU  - Seth L. Shipman
TI  - Reconstructing transcriptional histories by CRISPR acquisition of retron-based genetic barcodes
AID  - 10.1101/2021.08.11.455990
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.08.11.455990
4099  - http://biorxiv.org/content/early/2021/08/12/2021.08.11.455990.short
4100  - http://biorxiv.org/content/early/2021/08/12/2021.08.11.455990.full
AB  - Biological processes depend on the differential expression of genes over time, but methods to make true physical recordings of these processes are limited. Here we report a strategy for making time-ordered recordings of transcriptional events into living genomes. We do this via engineered RNA barcodes, based on prokaryotic retrons, which are reverse-transcribed into DNA and integrated into the genome using the CRISPR-Cas system. This approach enables the targeted recording of time-ordered transcriptional events in cells. The unidirectional integration of barcodes by CRISPR integrases enables reconstruction of transcriptional event timing based on a physical record via simple, logical rules rather than relying on pre-trained classifiers or post-hoc inferential methods.Competing Interest StatementS.L.S., G.M.C, M.G.S., and J.N. are named inventors on a patent application related to the technologies described in this work.