Woodworth, M. B., Girskis, K. M. & Walsh, C. A. Building a lineage from single cells: genetic techniques for cell lineage tracking. Nat. Rev. Genet. 18, 230–244 (2017).
Article PubMed PubMed Central CAS Google Scholar
Zon, L. I. Intrinsic and extrinsic control of haematopoietic stem-cell self-renewal. Nature 453, 306–313 (2008).
Article PubMed CAS Google Scholar
Livesey, F. J. & Cepko, C. L. Vertebrate neural cell-fate determination: lessons from the retina. Nat. Rev. Neurosci. 2, 109–118 (2001).
Article PubMed CAS Google Scholar
Schürch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182, 1341–1359.e19 (2020).
Article PubMed PubMed Central Google Scholar
Patel, S. H. et al. Lifelong multilineage contribution by embryonic-born blood progenitors. Nature 606, 747–753 (2022).
Article PubMed CAS Google Scholar
Nusser, A. et al. Developmental dynamics of two bipotent thymic epithelial progenitor types. Nature 606, 165–171 (2022).
Article PubMed PubMed Central CAS Google Scholar
Hu, B. et al. Origin and function of activated fibroblast states during zebrafish heart regeneration. Nat. Genet. 54, 1227–1237 (2022).
Article PubMed PubMed Central CAS Google Scholar
Quinn, J. J. et al. Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts. Science 371, eabc1944 (2021).
Article PubMed PubMed Central CAS 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
Chow, K.-H. K. et al. Imaging cell lineage with a synthetic digital recording system. Science 372, eabb3099 (2021).
Article PubMed CAS Google Scholar
McNamara, H. M., Solley, S. C., Adamson, B., Chan, M. M. & Toettcher, J. E. Recording morphogen signals reveals origins of gastruloid symmetry breaking. Nat. Cell Biol. https://doi.org/10.1038/s41556-024-01521-9 (2024).
Schmidt, F. et al. Noninvasive assessment of gut function using transcriptional recording sentinel cells. Science 376, eabm6038 (2022).
Article PubMed PubMed Central CAS Google Scholar
Farrell, J. A. et al. Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis. Science 360, eaar3131 (2018).
Article PubMed PubMed Central Google Scholar
Cao, J. et al. The single-cell transcriptional landscape of mammalian organogenesis. Nature 566, 496–502 (2019).
Article PubMed PubMed Central CAS Google Scholar
Li, H. et al. Fly Cell Atlas: a single-nucleus transcriptomic atlas of the adult fruit fly. Science 375, eabk2432 (2022).
Article PubMed PubMed Central CAS Google Scholar
Wagner, D. E. & Klein, A. M. Lineage tracing meets single-cell omics: opportunities and challenges. Nat. Rev. Genet. 21, 410–427 (2020).
Article PubMed PubMed Central CAS 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 PubMed CAS 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, F., Cherepkova, M. Y. & Platt, R. J. Transcriptional recording by CRISPR spacer acquisition from RNA. Nature 562, 380–385 (2018).
Article PubMed CAS Google Scholar
Kosuri, S. & Church, G. M. Large-scale de novo DNA synthesis: technologies and applications. Nat. Methods 11, 499–507 (2014).
Article PubMed PubMed Central CAS Google Scholar
Plesa, C., Sidore, A. M., Lubock, N. B., Zhang, D. & Kosuri, S. Multiplexed gene synthesis in emulsions for exploring protein functional landscapes. Science 359, 343–347 (2018).
Article PubMed PubMed Central CAS Google Scholar
Pryor, J. M. et al. Enabling one-pot Golden Gate assemblies of unprecedented complexity using data-optimized assembly design. PLoS ONE 15, e0238592 (2020).
Article PubMed PubMed Central CAS Google Scholar
Lau, C.-H., Tin, C. & Suh, Y. CRISPR-based strategies for targeted transgene knock-in and gene correction. Faculty Rev. 9, 20 (2020).
Merrick, C. A., Zhao, J. & Rosser, S. J. Serine integrases: advancing synthetic biology. ACS Synth. Biol. 7, 299–310 (2018).
Article PubMed CAS Google Scholar
Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).
Article PubMed PubMed Central CAS Google Scholar
Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013).
Article PubMed PubMed Central CAS Google Scholar
Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823–826 (2013).
Article PubMed PubMed Central CAS Google Scholar
Anzalone, A. V., Koblan, L. W. & Liu, D. R. Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors. Nat. Biotechnol. 38, 824–844 (2020).
Article PubMed CAS Google Scholar
Raj, B. et al. Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain. Nat. Biotechnol. 36, 442–450 (2018).
Article PubMed PubMed Central CAS Google Scholar
Askary, A. et al. In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription. Nat. Biotechnol. 38, 66–75 (2020).
Article PubMed CAS Google Scholar
Bouckaert, R. et al. BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 15, e1006650 (2019).
Article PubMed PubMed Central CAS Google Scholar
Qian, Y. et al. Programmable RNA sensing for cell monitoring and manipulation. Nature 610, 713–721 (2022).
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