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

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

    CAS PubMed PubMed Central Article Google Scholar

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

    ADS CAS PubMed Article Google Scholar

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

    ADS CAS PubMed Article Google Scholar

  • Shipman, SL, Nivala, J., Macklis, JD & Church, GM CRISPR–Cas encoding of a digital movie into the genomes of a population of living bacteria. nature 547345–349 (2017).

    ADS CAS PubMed PubMed Central Article Google Scholar

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

    CAS PubMed PubMed Central Article Google Scholar

  • Ceze, L., Nivala, J. & Strauss, K. Molecular digital data storage using DNA. nat. Rev. Gene 20456–466 (2019).

    CAS PubMed Article Google Scholar

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

    PubMed Article CAS Google Scholar

  • Sheth, RU, Yim, SS, Wu, FL & Wang, HH Multiplex recording of cellular events over time on CRISPR biological tape. 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 Article Google Scholar

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

    CAS PubMed PubMed Central Article Google Scholar

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

    PubMed PubMed Central Article CAS Google Scholar

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

    PubMed Article CAS Google Scholar

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

    CAS PubMed Article Google Scholar

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

    PubMed PubMed Central Article CAS Google Scholar

  • Simon, AJ, Morrow, BR & Ellington, AD Retroelement-based genome editing and evolution. ACS Synth. Biol. 72600–2611 (2018).

    CAS PubMed Article Google Scholar

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

    CAS PubMed PubMed Central Article Google Scholar

  • Schubert, MG et al. High-throughput functional variant screens via in vivo production of single-stranded DNA. process Natl Acad. Sci. USA 118e2018181118 (2021).

    CAS PubMed PubMed Central Article Google Scholar

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

    CAS PubMed Article Google Scholar

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

    PubMed PubMed Central Article CAS Google Scholar

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

    CAS PubMed PubMed Central Article Google Scholar

  • Nuñez, JK et al. Cas1–Cas2 complex formation mediates spacer acquisition during CRISPR–Cas adaptive immunity. nat. Struct. Mol. Biol. 21528–534 (2014).

    PubMed PubMed Central Article CAS 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 Article Google Scholar

  • Millman, A. et al. Bacterial retrons function in anti-phage defense. cell 1831551–1561 (2020).

    CAS PubMed Article Google Scholar

  • Bobonis, J. et al. Bacterial retrons encode 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 branched RNA-linked msDNA. science 2431033–1038 (1989).

    ADS CAS PubMed Article Google Scholar

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

    PubMed PubMed Central Article CAS Google Scholar

  • Bonnet, J., Subsoontorn, P. & Endy, D. Rewritable digital data storage in live cells via engineered control of recombination directionality. process Natl Acad. Sci. USA 1098884–8889 (2012).

    ADS CAS PubMed PubMed Central Article Google Scholar

  • Kim, S. et al. Selective loading and processing of prespacers for precise CRISPR adaptation. nature 579141–145 (2020).

    ADS CAS PubMed Article Google Scholar

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

    CAS PubMed Article Google Scholar

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

    CAS PubMed Article Google Scholar

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

    CAS PubMed Article Google Scholar

  • 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 Article Google Scholar

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

    CAS PubMed PubMed Central Article Google Scholar

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

    CAS PubMed Article Google Scholar

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

    Article Google Scholar

  • Stefansky, W. Rejecting outliers in factorial designs. Technometrics 14469-479 (1972).

    MATH Article Google Scholar

  • Hayflick, L. & Moorhead, PS The serial cultivation of human diploid cell strains. Exp. Cell. Res. 25585-621 (1961).

    CAS PubMed Article Google Scholar

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

    CAS PubMed PubMed Central Article Google Scholar

  • Yehl, K. & Lu, T. Scaling computation and memory in living cells. Curr. opinion Biomed. Eng. 4143–151 (2017).

    PubMed PubMed Central Article Google Scholar

  • Mosberg, JA, Gregg, CJ, Lajoie, MJ, Wang, HH & Church, GM Improving lambda Red genome engineering in Escherichia coli via rational removal of endogenous nucleases. PLoS ONE 7e44638 (2012).

    ADS CAS PubMed PubMed Central Article Google Scholar

  • Moore, SD In Strain Engineering: Methods and Protocols (ed. Williams, JA) 155–169 (Humana Press, 2011).

  • Datsenko, KA & Wanner, BL One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. process Natl Acad. Sci. USA 976640–6645 (2000).

    ADS CAS PubMed PubMed Central Article Google Scholar

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

    CAS PubMed PubMed Central Article Google Scholar

  • Leave a Reply

    %d bloggers like this: