Sheth, R. U. & Wang, H. H. DNA-based memory devices for recording cellular events. Nat. Rev. Genet. 19, 718–732 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

McKenna, A. et al. Whole-organism lineage tracing by combinatorial and cumulative genome editing. Science 353, aaf7907 (2016).

Article  PubMed  PubMed Central  Google Scholar 

Kalhor, R. et al. Developmental barcoding of whole mouse via homing CRISPR. Science 361, eaat9804 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Schmidt, S. T., Zimmerman, S. M., Wang, J., Kim, S. K. & Quake, S. R. Quantitative analysis of synthetic cell lineage tracing using nuclease barcoding. ACS Synth. Biol. https://doi.org/10.1021/acssynbio.6b00309 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Sheth, R. U., Yim, S. S., Wu, F. L. & Wang, H. H. Multiplex recording of cellular events over time on CRISPR biological tape. Science 358, 1457–1461 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Shipman, S. L., Nivala, J., Macklis, J. D. & Church, G. M. CRISPR–Cas encoding of a digital movie into the genomes of a population of living bacteria. Nature 547, 345–349 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Shipman, S. L., Nivala, J., Macklis, J. D. & Church, G. M. Molecular recordings by directed CRISPR spacer acquisition. Science 353, aaf1175 (2016).

Article  PubMed  PubMed Central  Google Scholar 

Schmidt, F., Cherepkova, M. Y. & Platt, R. J. Transcriptional recording by CRISPR spacer acquisition from RNA. Nature 562, 380–385 (2018).

Article  CAS  PubMed  Google Scholar 

Hwang, B. et al. Lineage tracing using a Cas9-deaminase barcoding system targeting endogenous L1 elements. Nat. Commun. 10, 1234 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Chan, M. M. et al. Molecular recording of mammalian embryogenesis. Nature 570, 77–82 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bowling, S. et al. An engineered CRISPR–Cas9 mouse line for simultaneous readout of lineage histories and gene expression profiles in single cells. Cell 181, 1410–1422.e27 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Alemany, A., Florescu, M., Baron, C. S., Peterson-Maduro, J. & van Oudenaarden, A. Whole-organism clone tracing using single-cell sequencing. Nature 556, 108–112 (2018).

Article  CAS  PubMed  Google Scholar 

Chow, K.-H. K. et al. Imaging cell lineage with a synthetic digital recording system. Science 372, eabb3099 (2021).

Article  CAS  PubMed  Google Scholar 

Loveless, T. B. et al. Lineage tracing and analog recording in mammalian cells by single-site DNA writing. Nat. Chem. Biol. 17, 739–747 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Choi, J. et al. A time-resolved, multi-symbol molecular recorder via sequential genome editing. Nature 608, 98–107 (2021).

Article  Google Scholar 

Perli, S. D., Cui, C. H. & Lu, T. K. Continuous genetic recording with self-targeting CRISPR–Cas in human cells. Science 353, aag0511 (2016).

Article  PubMed  Google Scholar 

Kalhor, R., Mali, P. & Church, G. M. Rapidly evolving homing CRISPR barcodes. Nat. Methods 14, 195–200 (2017).

Article  CAS  PubMed  Google Scholar 

Frieda, K. L. et al. Synthetic recording and in situ readout of lineage information in single cells. Nature 541, 107–111 (2017).

Article  CAS  PubMed  Google Scholar 

Tang, W. & Liu, D. R. Rewritable multi-event analog recording in bacterial and mammalian cells. Science 360, eaap8992 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Chen, W. et al. Multiplex genomic recording of enhancer and signal transduction activity in mammalian cells. Preprint at bioRxiv https://doi.org/10.1101/2021.11.05.467434 (2021).

Anzalone, A. V. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149–157 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Loveless, T. B. et al. Molecular recording of sequential cellular events into DNA. Preprint at bioRxiv https://doi.org/10.1101/2021.11.05.467507 (2024).

Chen, P. J. et al. Enhanced prime editing systems by manipulating cellular determinants of editing outcomes. Cell 184, 5635–5652.e29 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A. & Liu, D. R. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533, 420–424 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cabera, A. et al. The sound of silence: transgene silencing in mammalian cell engineering. Cell Syst. 13, 950–973 (2022).

Article  CAS  PubMed Central  Google Scholar 

Gould, S. I. et al. High-throughput evaluation of genetic variants with prime editing sensor libraries. Nat. Biotechnol. https://doi.org/10.1038/s41587-024-02172-9 (2024).

Yan, J. et al. Improving prime editing with an endogenous small RNA-binding protein. Nature 628, 639–647 (2024).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Shannon, C. E. A mathematical theory of communication. Bell Syst. Tech. J. 27, 379–423 (1948).

Article  Google Scholar 

Jaccard, P. The distribution of the flora in the alpine zone. New Phytol. 11, 37–50 (1912).

Article  Google Scholar 

Schmidt, F. et al. Noninvasive assessment of gut function using transcriptional recording sentinel cells. Science 376, eabm6038 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bhattarai-Kline, S. et al. Recording gene expression order in DNA by CRISPR addition of retron barcodes. Nature 608, 217–225 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nambiar, T. S., Baudrier, L., Billon, P. & Ciccia, A. CRISPR-based genome editing through the lens of DNA repair. Mol. Cell 82, 348–388 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Balakrishnan, L. & Bambara, R. A. Flap Endonuclease 1. Annu. Rev. Biochem. 82, 119–138 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sallmyr, A., Rashid, I., Bhandari, S. K., Naila, T. & Tomkinson, A. E. Human DNA ligases in replication and repair. DNA Repair 93, 102908 (2020).

Article