Simon, AJ, Ellington, AD & Finkelstein, IJ Retrons and their applications in genome engineering. Nucleic Acids Res. 4711007–11019 (2019).
Barrangou, R. et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 3151709-1712 (2007).
Church, GM, Gao, Y. & Kosuri, S. Next-generation digital information storage in DNA. Science 3371628-1628 (2012).
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).
Yim, SS et al. Robust direct storage of digital to biological data in living cells. Nat. Chem. Biol. 17246-253 (2021).
Ceze, L., Nivala, J. & Strauss, K. Molecular digital data storage using DNA. Nat. Reverend Genet. 20456–466 (2019).
Roquet, N., Soleimany, AP, Ferris, AC, Aaronson, S. & Lu, TK Recombinase-based synthetic state machines in living cells. Science 353aad8559 (2016).
Sheth, RU, Yim, SS, Wu, FL & Wang, HH Multiplex recording of cellular events over time on CRISPR biostrip. Science 3581457-1461 (2017).
Schmidt, F., Cherepkova, MY & Platt, RJ Transcriptional recording by CRISPR spacer acquisition from RNA. Nature 562380–385 (2018).
Wagner, DE & Klein, AM Lineage tracing meets single-cell omics: opportunities and challenges. Nat. Reverend Genet. 21410–427 (2020).
Street, K. et al. Slingshot: cell lineage and pseudo-temporal inference for single-cell transcriptomics. BMC Genomics 19477 (2018).
Perli, SD, Cui, CH & Lu, TK Continuous genetic recording with self-targeting CRISPR-Cas in human cells. Science 353aag0511 (2016).
Park, J. et al. Recording of elapsed time and temporal information of biological events using Cas9. Cell 1841047-1063 (2021).
Shipman, SL, Nivala, J., Macklis, JD & Church, GM Molecular recordings by directed acquisition of CRISPR spacers. Science 353aaf1175 (2016).
Simon, AJ, Morrow, BR & Ellington, AD Retroelement-based genome editing and evolution. Synth ACS. Biol. seven2600–2611 (2018).
Sharon, E. et al. Functional genetic variants revealed by precise massively parallel genome editing. Cell 175544-557 (2018).
Schubert, MG et al. High-throughput functional variant screens via in vivo single-stranded DNA production. proc. Natl Acad. Know United States 118e2018181118 (2021).
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).
Farzadfard, F. & Lu, TK Genomically-encoded analog memory with precise in vivo DNA writing in live cell populations. Science 3461256272 (2014).
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).
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).
Wang, J. et al. Structural and mechanistic basis of PAM-dependent spacer acquisition in CRISPR-Cas systems. Cell 163840–853 (2015).
Millman, A. et al. Bacterial retrons play a role in anti-phage defense. Cell 1831551-1561 (2020).
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).
Silas, S. et al. Direct acquisition of the CRISPR spacer from RNA by a natural reverse transcriptase-Cas1 fusion protein. Science 351aad4234 (2016).
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).
Kim, S. et al. Selective loading and processing of pre-spacers for precise CRISPR matching. Nature 579141–145 (2020).
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).
Chapman, KB & Boeke, JD Isolation and characterization of the gene encoding the yeast debranching enzyme. Cell 65483–492 (1991).
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).
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).
Han, ES et al. Exonuclease RecJ: substrates, products and interaction with SSB. Nucleic Acids Res. 341084–1091 (2006).
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).
Grubbs, FE Procedures for detecting outliers in samples. Technometrics 111–21 (1969).
Stefansky, W. Rejecting Outliers in Factorial Designs. Technometrics 14469–479 (1972).
Hayflick, L. & Moorhead, PS Serial culture of human diploid cell strains. Exp. Cell. Res. 25585–621 (1961).
Yang, L. et al. Permanent genetic memory with a capacity > 1 byte. Nat. Methods 111261-1266 (2014).
Yehl, K. & Lu, T. Scaling computation and memory in living cells. Running. Notice. Biomedical. Eng. 4143-151 (2017).
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).
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).
Rogers, JK et al. Synthetic biosensors for precise genetic control and real-time monitoring of metabolites. Nucleic Acids Res. 437648–7660 (2015).