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

Author

Listed:
  • Santi Bhattarai-Kline

    (Gladstone Institute of Data Science and Biotechnology)

  • Sierra K. Lear

    (Gladstone Institute of Data Science and Biotechnology
    University of California, San Francisco and Berkeley)

  • Chloe B. Fishman

    (Gladstone Institute of Data Science and Biotechnology)

  • Santiago C. Lopez

    (Gladstone Institute of Data Science and Biotechnology
    University of California, San Francisco and Berkeley)

  • Elana R. Lockshin

    (Duke University Medical Center)

  • Max G. Schubert

    (Harvard Medical School
    Harvard University)

  • Jeff Nivala

    (University of Washington)

  • George M. Church

    (Harvard Medical School
    Harvard University)

  • Seth L. Shipman

    (Gladstone Institute of Data Science and Biotechnology
    University of California, San Francisco)

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.

Suggested Citation

  • Santi Bhattarai-Kline & Sierra K. Lear & Chloe B. Fishman & Santiago C. Lopez & Elana R. Lockshin & Max G. Schubert & Jeff Nivala & George M. Church & Seth L. Shipman, 2022. "Recording gene expression order in DNA by CRISPR addition of retron barcodes," Nature, Nature, vol. 608(7921), pages 217-225, August.
    • Handle: RePEc:nat:nature:v:608:y:2022:i:7921:d:10.1038_s41586-022-04994-6
    DOI: 10.1038/s41586-022-04994-6
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