The lives of cells, recorded

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).

Article  Google Scholar 

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).

Comments (0)

No login
gif