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

  • Simon, AJ, Ellington, AD & Finkelstein, IJ Retrons and their applications in genome engineering. Nucleic Acids Res. 4711007–11019 (2019).

    CAS PubMed PubMed Central Google Scholar Article

  • Barrangou, R. et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 3151709-1712 (2007).

    ADS CAS PubMed Google Scholar Article

  • Church, GM, Gao, Y. & Kosuri, S. Next-generation digital information storage in DNA. Science 3371628-1628 (2012).

    ADS CAS PubMed Google Scholar Article

  • Shipman, SL, Nivala, J., Macklis, JD & Church, GM CRISPR encoding–Case of a digital movie in the genomes of a living bacterial population. Nature 547345–349 (2017).

    ADS CAS PubMed PubMed Central Article Google Scholar

  • Yim, SS et al. Robust direct storage of digital to biological data in living cells. Nat. Chem. Biol. 17246-253 (2021).

    CAS PubMed PubMed Central Google Scholar Article

  • Ceze, L., Nivala, J. & Strauss, K. Molecular digital data storage using DNA. Nat. Reverend Genet. 20456–466 (2019).

    CAS PubMed Google Scholar Article

  • Roquet, N., Soleimany, AP, Ferris, AC, Aaronson, S. & Lu, TK Recombinase-based synthetic state machines in living cells. Science 353aad8559 (2016).

    PubMed CAS Google Scholar Article

  • Sheth, RU, Yim, SS, Wu, FL & Wang, HH Multiplex recording of cellular events over time on CRISPR biostrip. Science 3581457-1461 (2017).

    ADS CAS PubMed PubMed Central Article Google Scholar

  • Schmidt, F., Cherepkova, MY & Platt, RJ Transcriptional recording by CRISPR spacer acquisition from RNA. Nature 562380–385 (2018).

    ADS CAS PubMed Google Scholar Article

  • Wagner, DE & Klein, AM Lineage tracing meets single-cell omics: opportunities and challenges. Nat. Reverend Genet. 21410–427 (2020).

    CAS PubMed PubMed Central Google Scholar Article

  • Street, K. et al. Slingshot: cell lineage and pseudo-temporal inference for single-cell transcriptomics. BMC Genomics 19477 (2018).

    PubMed PubMed Central CAS Article Google Scholar

  • Perli, SD, Cui, CH & Lu, TK Continuous genetic recording with self-targeting CRISPR-Cas in human cells. Science 353aag0511 (2016).

    PubMed CAS Google Scholar Article

  • Park, J. et al. Recording of elapsed time and temporal information of biological events using Cas9. Cell 1841047-1063 (2021).

    CAS PubMed Google Scholar Article

  • Shipman, SL, Nivala, J., Macklis, JD & Church, GM Molecular recordings by directed acquisition of CRISPR spacers. Science 353aaf1175 (2016).

    PubMed PubMed Central CAS Article Google Scholar

  • Simon, AJ, Morrow, BR & Ellington, AD Retroelement-based genome editing and evolution. Synth ACS. Biol. seven2600–2611 (2018).

    CAS PubMed Google Scholar Article

  • Sharon, E. et al. Functional genetic variants revealed by precise massively parallel genome editing. Cell 175544-557 (2018).

    CAS PubMed PubMed Central Google Scholar Article

  • Schubert, MG et al. High-throughput functional variant screens via in vivo single-stranded DNA production. proc. Natl Acad. Know United States 118e2018181118 (2021).

    CAS PubMed PubMed Central Google Scholar Article

  • Lopez, SC, Crawford, KD, Lear, SK, Bhattarai-Kline, S. & Shipman, SL Precise genome editing in realms of life using retron-derived DNA. Nat. Chem. Biol. 18199–206 (2022).

    CAS PubMed Google Scholar Article

  • Farzadfard, F. & Lu, TK Genomically-encoded analog memory with precise in vivo DNA writing in live cell populations. Science 3461256272 (2014).

    PubMed PubMed Central CAS Article Google Scholar

  • Yosef, I., Goren, MG & Qimron, U. Essential proteins and DNA elements for the CRISPR adaptation process in Escherichia coli. Nucleic Acids Res. 405569–5576 (2012).

    CAS PubMed PubMed Central Google Scholar Article

  • Nuñez, JK et al. Formation of the Cas1–Cas2 complex mediates spacer acquisition during CRISPR–Cas adaptive immunity. Nat. Structure. Mol. Biol. 21528–534 (2014).

    PubMed PubMed Central CAS Article Google Scholar

  • Wang, J. et al. Structural and mechanistic basis of PAM-dependent spacer acquisition in CRISPR-Cas systems. Cell 163840–853 (2015).

    CAS PubMed Google Scholar Article

  • Millman, A. et al. Bacterial retrons play a role in anti-phage defense. Cell 1831551-1561 (2020).

    CAS PubMed Google Scholar Article

  • Bobonis, J. et al. Bacterial retrons code for tripartite toxin/antitoxin systems. Preprint at bioRxiv https://doi.org/10.1101/2020.06.22.160168 (2020).

  • Lampson, BC et al. Reverse transcriptase in a clinical strain of Escherichia coli: production of msDNA linked to branched RNA. Science 2431033-1038 (1989).

    ADS CAS PubMed Google Scholar Article

  • Silas, S. et al. Direct acquisition of the CRISPR spacer from RNA by a natural reverse transcriptase-Cas1 fusion protein. Science 351aad4234 (2016).

    PubMed PubMed Central CAS Article Google Scholar

  • Bonnet, J., Subsoontorn, P. & Endy, D. Storage of rewritable digital data in living cells via engineering control of recombination directionality. proc. Natl Acad. Know United States 1098884–8889 (2012).

    ADS CAS PubMed PubMed Central Article Google Scholar

  • Kim, S. et al. Selective loading and processing of pre-spacers for precise CRISPR matching. Nature 579141–145 (2020).

    ADS CAS PubMed Google Scholar Article

  • Ramachandran, A., Summerville, L., Learn, BA, DeBell, L. & Bailey, S. Processing and integration of functional prespacers into the Escherichia coli The CRISPR system depends on the exonucleases of the bacterial host. J. Biol. Chem. 2953403–3414 (2020).

    CAS PubMed Google Scholar Article

  • Chapman, KB & Boeke, JD Isolation and characterization of the gene encoding the yeast debranching enzyme. Cell 65483–492 (1991).

    CAS PubMed Google Scholar Article

  • Lim, D. Structure and biosynthesis of unbranched multicopy single-stranded DNA by reverse transcriptase in a clinical setting Eschechia coli isolate. Mol. Microbiol. 63531–3542 (1992).

    CAS PubMed Google Scholar Article

  • Jung, H., Liang, J., Jung, Y. & Lim, D. Characterization of cell death in Escherichia coli mediated by XseA, a large subunit of exonuclease VII. J. Microbiol. 53820–828 (2015).

    CAS PubMed Google Scholar Article

  • Han, ES et al. Exonuclease RecJ: substrates, products and interaction with SSB. Nucleic Acids Res. 341084–1091 (2006).

    CAS PubMed PubMed Central Google Scholar Article

  • Meyer, AJ, Segall-Shapiro, TH, Glassey, E., Zhang, J. & Voigt, CA Escherichia coli “Puppet” strains with 12 highly optimized small molecule sensors. Nat. Chem. Biol. 15196-204 (2019).

    CAS PubMed Google Scholar Article

  • Grubbs, FE Procedures for detecting outliers in samples. Technometrics 111–21 (1969).

    Google Scholar article

  • Stefansky, W. Rejecting Outliers in Factorial Designs. Technometrics 14469–479 (1972).

    MATH Google Scholar Article

  • Hayflick, L. & Moorhead, PS Serial culture of human diploid cell strains. Exp. Cell. Res. 25585–621 (1961).

    CAS PubMed Google Scholar Article

  • Yang, L. et al. Permanent genetic memory with a capacity > 1 byte. Nat. Methods 111261-1266 (2014).

    CAS PubMed PubMed Central Google Scholar Article

  • Yehl, K. & Lu, T. Scaling computation and memory in living cells. Running. Notice. Biomedical. Eng. 4143-151 (2017).

    PubMed PubMed Central ArticleGoogle Scholar

  • Mosberg, JA, Gregg, CJ, Lajoie, MJ, Wang, HH & Church, GM Improved lambda red genome engineering in Escherichia coli via the rational elimination of endogenous nucleases. PLOS ONE sevene44638 (2012).

    ADS CAS PubMed PubMed Central Article Google Scholar

  • Moore, SD In Stress engineering: methods and protocols (Williams, JA ed.) 155–169 (Humana Press, 2011).

  • Datsenko, KA & Wanner, BL One-step knockout of chromosomal genes in Escherichia coli K-12 using PCR products. proc. Natl Acad. Know United States 976640–6645 (2000).

    ADS CAS PubMed PubMed Central Article Google Scholar

  • Rogers, JK et al. Synthetic biosensors for precise genetic control and real-time monitoring of metabolites. Nucleic Acids Res. 437648–7660 (2015).

    CAS PubMed PubMed Central Google Scholar Article

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