The DOI matches its Crossref record; 30 of the 30 references it cites were found in a registry or an index.
Tracking genome engineering outcome at individual DNA breakpoints
Open accessAbstract
Site-specific genome engineering technologies are increasingly important tools in the postgenomic era, where biotechnological objectives often require organisms with precisely modified genomes. Rare-cutting endonucleases, through their capacity to create a targeted DNA strand break, are one of the most promising of these technologies. However, realizing the full potential of nuclease-induced genome engineering requires a detailed understanding of the variables that influence resolution of nuclease-induced DNA breaks. Here we present a genome engineering reporter system, designated 'traffic light', that supports rapid flow-cytometric analysis of repair pathway choice at individual DNA breaks, quantitative tracking of nuclease expression and donor template delivery, and high-throughput screens for factors that bias the engineering outcome. We applied the traffic light system to evaluate the efficiency and outcome of nuclease-induced genome engineering in human cell lines and identified strategies to facilitate isolation of cells in which a desired engineering outcome has occurred.
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Cites
ATM and ATR Substrate Analysis Reveals Extensive Protein Networks Responsive to DNA Damage
Matsuoka, S., Ballif, B. A., Smogorzewska, A., McDonald, E. R., Hurov, K. E., Luo, J., Bakalarski, C. E., Zhao, Z., Solimini, N., Lerenthal, Y., et al. (2007) · Science · doi:10.1126/science.1140321 · Cited by 3,075
XRCC3 promotes homology-directed repair of DNA damage in mammalian cells
Pierce, A. J., Johnson, R. D., Thompson, L. H., & Jasin, M. (1999) · Genes & Development · doi:10.1101/gad.13.20.2633 · Cited by 1,379
Regulation of DNA double-strand break repair pathway choice
Shrivastav, M., De Haro, L. P., & Nickoloff, J. A. (2008) · Cell Research · doi:10.1038/cr.2007.111 · Cited by 1,329
Regulation of DNA repair throughout the cell cycle
Branzei, D., & Foiani, M. (2008) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2351 · Cited by 1,228
Single-strand break repair and genetic disease
Caldecott, K. W. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2380 · Cited by 1,034
Alternative-NHEJ Is a Mechanistically Distinct Pathway of Mammalian Chromosome Break Repair
Bennardo, N., Cheng, A., Huang, N., & Stark, J. M. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000110 · Cited by 870
Chimeric nucleases stimulate gene targeting in human cells
Porteus, M. H., & Baltimore, D. (2003) · Science · doi:10.1126/science.1078395 · Cited by 741
Mammalian Expression of Infrared Fluorescent Proteins Engineered from a Bacterial Phytochrome
Shu, X., Royant, A., Lin, M. Z., Aguilera, T. A., Lev-Ram, V., Steinbach, P. A., & Tsien, R. Y. (2009) · Science · doi:10.1126/science.1168683 · Cited by 675
Gene targeting using zinc finger nucleases
Porteus, M. H., & Carroll, D. (2005) · Nature Biotechnology · doi:10.1038/nbt1125 · Cited by 641
Durai, S. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki912 · Cited by 522
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Porteus, M. H. (2019) · New England Journal of Medicine · doi:10.1056/nejmra1800729 · Cited by 229
Sather, B. D., Romano Ibarra, G. S., Sommer, K., Curinga, G., Hale, M., Khan, I. F., Singh, S., Song, Y., Gwiazda, K., Sahni, J., et al. (2015) · Science Translational Medicine · doi:10.1126/scitranslmed.aac5530 · Cited by 223
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Metadata
- Authors
- Certo, M. T., Ryu, B. Y., Annis, J. E., Garibov, M., Jarjour, J., Rawlings, D. J., & Scharenberg, A. M.
- Venue
- Nature Methods
- Published
- 2011-07-10
- Volume
- 8
- Issue
- 8
- Pages
- 671-676
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2020091112
- Cited by
- 318
- References
- 30
- FWCI
- 6.00
- Type
- journal article
- Language
- en
- Open access
- green
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