Multiplexed Targeted Genome Engineering Using a Universal Nuclease-Assisted Vector Integration System

ACS Synthetic Biology

Volumn 5, Issue 7, 2016, Pages 582-588

  Brown, Alexander ^a   Woods, Wendy S ^a   Perez Pinera, Pablo ^a  

^a University of Illinois at Urbana Champaign   (United States)

Author keywords

CRISPR; DNA recombination; gene editing; genome engineering; synthetic biology; TALEN; targeted genome integration

Indexed keywords

DNA; NUCLEASE; BACTERIAL PROTEIN; CAS9 ENDONUCLEASE STREPTOCOCCUS PYOGENES; CORTACTIN; CRISPR ASSOCIATED ENDONUCLEASE CAS9; CRISPR-CAS SYSTEM GUIDE RNA; CTTN PROTEIN, HUMAN; ENDONUCLEASE; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; GREEN FLUORESCENT PROTEIN; TRANSCRIPTION ACTIVATOR LIKE EFFECTOR NUCLEASE;

ARTICLE; CONTROLLED STUDY; DNA INTEGRATION; EMBRYO; GENE DISRUPTION; GENE EDITING; GENE INACTIVATION; GENETIC ENGINEERING; GENETIC TRANSFECTION; GENOME ANALYSIS; GENOME ENGINEERING; HCT116 CELL LINE; HEK293 CELL LINE; HUMAN; HUMAN CELL; MOLECULAR GENETICS; PRIORITY JOURNAL; SYNTHETIC BIOLOGY; GENE KNOCKOUT; GENE VECTOR; GENETICS; GENOME; HCT 116 CELL LINE; PROCEDURES; TRANSGENE;

BACTERIAL PROTEINS; CORTACTIN; CRISPR-ASSOCIATED PROTEIN 9; ENDONUCLEASES; GENE EDITING; GENE KNOCKOUT TECHNIQUES; GENETIC ENGINEERING; GENETIC VECTORS; GENOME; GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (PHOSPHORYLATING); GREEN FLUORESCENT PROTEINS; HCT116 CELLS; HUMANS; RNA, GUIDE, CRISPR-CAS SYSTEMS; TRANSCRIPTION ACTIVATOR-LIKE EFFECTOR NUCLEASES; TRANSFECTION; TRANSGENES;

EID: 84978665442     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/acssynbio.6b00056     Document Type: Article

References (26)

1. Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., and Zhang, F. (2013) Multiplex genome engineering using CRISPR/Cas systems Science 339, 819-823 10.1126/science.1231143
2. Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., and Charpentier, E. (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity Science 337, 816-821 10.1126/science.1225829
3. Jinek, M., East, A., Cheng, A., Lin, S., Ma, E., and Doudna, J. (2013) RNA-programmed genome editing in human cells eLife 2, e00471 10.7554/eLife.00471
4. Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J. E., Norville, J. E., and Church, G. M. (2013) RNA-guided human genome engineering via Cas9 Science 339, 823-826 10.1126/science.1232033
5. Doudna, J. A. and Charpentier, E. (2014) Genome editing. The new frontier of genome engineering with CRISPR-Cas9 Science 346, 1258096 10.1126/science.1258096
6. Zhang, Y., Ge, X., Yang, F., Zhang, L., Zheng, J., Tan, X., Jin, Z. B., Qu, J., and Gu, F. (2014) Comparison of non-canonical PAMs for CRISPR/Cas9-mediated DNA cleavage in human cells Sci. Rep. 4, 5405 10.1038/srep05405
7. Carroll, D. (2014) Genome engineering with targetable nucleases Annu. Rev. Biochem. 83, 409-439 10.1146/annurev-biochem-060713-035418
8. Sander, J. D. and Joung, J. K. (2014) CRISPR-Cas systems for editing, regulating and targeting genomes Nat. Biotechnol. 32, 347-355 10.1038/nbt.2842
9. Li, H., Haurigot, V., Doyon, Y., Li, T., Wong, S. Y., Bhagwat, A. S., Malani, N., Anguela, X. M., Sharma, R., Ivanciu, L., Murphy, S. L., Finn, J. D., Khazi, F. R., Zhou, S., Paschon, D. E., Rebar, E. J., Bushman, F. D., Gregory, P. D., Holmes, M. C., and High, K. A. (2011) In vivo genome editing restores haemostasis in a mouse model of haemophilia Nature 475, 217-221 10.1038/nature10177
10. Connelly, J. P., Barker, J. C., Pruett-Miller, S., and Porteus, M. H. (2010) Gene correction by homologous recombination with zinc finger nucleases in primary cells from a mouse model of a generic recessive genetic disease Mol. Ther. 18, 1103-1110 10.1038/mt.2010.57
11. Doyon, J. B., Zeitler, B., Cheng, J., Cheng, A. T., Cherone, J. M., Santiago, Y., Lee, A. H., Vo, T. D., Doyon, Y., Miller, J. C., Paschon, D. E., Zhang, L., Rebar, E. J., Gregory, P. D., Urnov, F. D., and Drubin, D. G. (2011) Rapid and efficient clathrin-mediated endocytosis revealed in genome-edited mammalian cells Nat. Cell Biol. 13, 331-337 10.1038/ncb2175
12. Savic, D., Partridge, E. C., Newberry, K. M., Smith, S. B., Meadows, S. K., Roberts, B. S., Mackiewicz, M., Mendenhall, E. M., and Myers, R. M. (2015) CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins Genome Res. 25, 1581-1589 10.1101/gr.193540.115
13. Byrne, S. M., Ortiz, L., Mali, P., Aach, J., and Church, G. M. (2015) Multi-kilobase homozygous targeted gene replacement in human induced pluripotent stem cells Nucleic Acids Res. 43, e21 10.1093/nar/gku1246
14. Auer, T. O., Duroure, K., De Cian, A., Concordet, J. P., and Del Bene, F. (2014) Highly efficient CRISPR/Cas9-mediated knock-in in zebrafish by homology-independent DNA repair Genome Res. 24, 142-153 10.1101/gr.161638.113
15. Nakade, S., Tsubota, T., Sakane, Y., Kume, S., Sakamoto, N., Obara, M., Daimon, T., Sezutsu, H., Yamamoto, T., Sakuma, T., and Suzuki, K. T. (2014) Microhomology-mediated end-joining-dependent integration of donor DNA in cells and animals using TALENs and CRISPR/Cas9 Nat. Commun. 5, 5560 10.1038/ncomms6560
16. Kimura, Y., Oda, M., Nakatani, T., Sekita, Y., Monfort, A., Wutz, A., Mochizuki, H., and Nakano, T. (2015) CRISPR/Cas9-mediated reporter knock-in in mouse haploid embryonic stem cells Sci. Rep. 5, 10710 10.1038/srep10710
17. Sakuma, T., Takenaga, M., Kawabe, Y., Nakamura, T., Kamihira, M., and Yamamoto, T. (2015) Homologous Recombination-Independent Large Gene Cassette Knock-in in CHO Cells Using TALEN and MMEJ-Directed Donor Plasmids Int. J. Mol. Sci. 16, 23849-23866 10.3390/ijms161023849
18. Lackner, D. H., Carre, A., Guzzardo, P. M., Banning, C., Mangena, R., Henley, T., Oberndorfer, S., Gapp, B. V., Nijman, S. M., Brummelkamp, T. R., and Burckstummer, T. (2015) A generic strategy for CRISPR-Cas9-mediated gene tagging Nat. Commun. 6, 10237 10.1038/ncomms10237
19. Sakuma, T., Nakade, S., Sakane, Y., Suzuki, K. T., and Yamamoto, T. (2016) MMEJ-assisted gene knock-in using TALENs and CRISPR-Cas9 with the PITCh systems Nat. Protoc. 11, 118-133 10.1038/nprot.2015.140
20. Tsai, S. Q., Zheng, Z., Nguyen, N. T., Liebers, M., Topkar, V. V., Thapar, V., Wyvekens, N., Khayter, C., Iafrate, A. J., Le, L. P., Aryee, M. J., and Joung, J. K. (2015) GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases Nat. Biotechnol. 33, 187-197 10.1038/nbt.3117
21. Hsu, P. D., Scott, D. A., Weinstein, J. A., Ran, F. A., Konermann, S., Agarwala, V., Li, Y., Fine, E. J., Wu, X., Shalem, O., Cradick, T. J., Marraffini, L. A., Bao, G., and Zhang, F. (2013) DNA targeting specificity of RNA-guided Cas9 nucleases Nat. Biotechnol. 31, 827-832 10.1038/nbt.2647
22. Bolukbasi, M. F., Gupta, A., Oikemus, S., Derr, A. G., Garber, M., Brodsky, M. H., Zhu, L. J., and Wolfe, S. A. (2015) DNA-binding-domain fusions enhance the targeting range and precision of Cas9 Nat. Methods 12, 1150-1156 10.1038/nmeth.3624
23. Slaymaker, I. M., Gao, L., Zetsche, B., Scott, D. A., Yan, W. X., and Zhang, F. (2016) Rationally engineered Cas9 nucleases with improved specificity Science 351, 84 10.1126/science.aad5227
24. Fu, Y., Sander, J. D., Reyon, D., Cascio, V. M., and Joung, J. K. (2014) Improving CRISPR-Cas nuclease specificity using truncated guide RNAs Nat. Biotechnol. 32, 279-284 10.1038/nbt.2808
25. Perez-Pinera, P., Kocak, D. D., Vockley, C. M., Adler, A. F., Kabadi, A. M., Polstein, L. R., Thakore, P. I., Glass, K. A., Ousterout, D. G., Leong, K. W., Guilak, F., Crawford, G. E., Reddy, T. E., and Gersbach, C. A. (2013) RNA-guided gene activation by CRISPR-Cas9-based transcription factors Nat. Methods 10, 973-976 10.1038/nmeth.2600
26. Guschin, D. Y., Waite, A. J., Katibah, G. E., Miller, J. C., Holmes, M. C., and Rebar, E. J. (2010) A rapid and general assay for monitoring endogenous gene modification Methods Mol. Biol. 649, 247-256 10.1007/978-1-60761-753-2-15