Recording gene expression order in DNA by CRISPR addition of retron barcodes

Santi Bhattarai-Kline, Sierra K. Lear, Chloe B. Fishman, Santiago C. Lopez, Elana R. Lockshin, Max G. Schubert, Jeff Nivala, George M. Church and Seth L. Shipman ()
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Santi Bhattarai-Kline: Gladstone Institute of Data Science and Biotechnology
Sierra K. Lear: Gladstone Institute of Data Science and Biotechnology
Chloe B. Fishman: Gladstone Institute of Data Science and Biotechnology
Santiago C. Lopez: Gladstone Institute of Data Science and Biotechnology
Elana R. Lockshin: Duke University Medical Center
Max G. Schubert: Harvard Medical School
Jeff Nivala: University of Washington
George M. Church: Harvard Medical School
Seth L. Shipman: Gladstone Institute of Data Science and Biotechnology

Nature, 2022, vol. 608, issue 7921, 217-225

Abstract: Abstract Biological processes depend on the differential expression of genes over time, but methods to make physical recordings of these processes are limited. Here we report a molecular system for making time-ordered recordings of transcriptional events into living genomes. We do this through engineered RNA barcodes, based on prokaryotic retrons1, that are reverse transcribed into DNA and integrated into the genome using the CRISPR–Cas system2. The unidirectional integration of barcodes by CRISPR integrases enables reconstruction of transcriptional event timing based on a physical record through simple, logical rules rather than relying on pretrained classifiers or post hoc inferential methods. For disambiguation in the field, we will refer to this system as a Retro-Cascorder.

Date: 2022
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DOI: 10.1038/s41586-022-04994-6

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