Synthesis of an arrayed sgRNA library targeting the human genome

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Schmidt, Tobias ^a   Schmid Burgk, Jonathan L ^a   Hornung, Veit ^a  

^a UNIVERSITY HOSPITAL BONN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CRISPR ASSOCIATED PROTEIN; GUIDE RNA;

ANIMAL; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CRISPR CAS SYSTEM; EXON; GENE INACTIVATION; GENE LIBRARY; GENETICS; HEK293 CELL LINE; HUMAN; HUMAN GENOME; METABOLISM; MOLECULAR CLONING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROCEDURES;

ANIMALS; BASE SEQUENCE; CLONING, MOLECULAR; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; CRISPR-ASSOCIATED PROTEINS; CRISPR-CAS SYSTEMS; EXONS; GENE KNOCKOUT TECHNIQUES; GENE LIBRARY; GENOME, HUMAN; HEK293 CELLS; HUMANS; MOLECULAR SEQUENCE DATA; RNA, GUIDE;

EID: 84943635310     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep14987     Document Type: Article

References (40)

1. Horvath, P. & Barrangou, R. CRISPR/Cas, the immune system of bacteria and archaea. Science 327, 167-170, doi: 10.1126/science.1179555 (2010).
2. Wiedenheft, B., Sternberg, S. H. & Doudna, J. A. RNA-guided genetic silencing systems in bacteria and archaea. Nature 482, 331-338, doi: 10.1038/nature10886 (2012).
3. Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821, doi: 10.1126/science.1225829 (2012).
4. Jiang, W., Bikard, D., Cox, D., Zhang, F. & Marraffini, L. A. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol 31, 233-239, doi: 10.1038/nbt.2508 (2013).
5. Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823-826, doi: 10.1126/science.1232033 (2013).
6. Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819-823, doi: 10.1126/science.1231143 (2013).
7. Hwang, W. Y. et al. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol 31, 227-229, doi: 10.1038/nbt.2501 (2013).
8. Jinek, M. et al. RNA-programmed genome editing in human cells. Elife 2, e00471, doi: 10.7554/eLife.00471 (2013).
9. Cho, S. W., Kim, S., Kim, J. M. & Kim, J. S. Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat Biotechnol 31, 230-232, doi: 10.1038/nbt.2507 (2013).
10. Chang, N. et al. Genome editing with RNA-guided Cas9 nuclease in zebrafish embryos. Cell Res 23, 465-472, doi: 10.1038/cr.2013.45 (2013).
11. Wang, T., Wei, J. J., Sabatini, D. M. & Lander, E. S. Genetic screens in human cells using the CRISPR-Cas9 system. Science 343, 80-84, doi: 10.1126/science.1246981 (2014).
12. Shalem, O. et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343, 84-87, doi: 10.1126/science.1247005 (2014).
13. Koike-Yusa, H., Li, Y., Tan, E. P., Velasco-Herrera Mdel, C. & Yusa, K. Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library. Nat Biotechnol 32, 267-273, doi: 10.1038/nbt.2800 (2014).
14. Aslanidis, C. & de Jong, P. J. Ligation-independent cloning of PCR products (LIC-PCR). Nucleic Acids Res 18, 6069-6074 (1990).
15. Schmid-Burgk, J. L. et al. Rapid hierarchical assembly of medium-size DNA cassettes. Nucleic Acids Res 40, e92, doi: 10.1093/nar/gks236 (2012).
16. Schmid-Burgk, J. L., Schmidt, T., Kaiser, V., Honing, K. & Hornung, V. A ligation-independent cloning technique for highthroughput assembly of transcription activator-like effector genes. Nat Biotechnol 31, 76-81, doi: 10.1038/nbt.2460 (2013).
17. Erlich, Y. et al. DNA Sudoku-harnessing high-throughput sequencing for multiplexed specimen analysis. Genome research 19, 1243-1253, doi: 10.1101/gr.092957.109 (2009).
18. Burckstummer, T. et al. A reversible gene trap collection empowers haploid genetics in human cells. Nature methods 10, 965-971, doi: 10.1038/nmeth.2609 (2013).
19. Schmid-Burgk, J. L. et al. Out Knocker: a web tool for rapid and simple genotyping of designer nuclease edited cell lines. Genome research doi: 10.1101/gr.176701.114 (2014).
20. Pelka, K. et al. Cutting Edge: The UNC93B1 Tyrosine-Based Motif Regulates Trafficking and TLR Responses via Separate Mechanisms. J Immunol 193, 3257-3261, doi: 10.4049/jimmunol.1301886 (2014).
21. Mankan, A. K. et al. Cytosolic RNA:DNA hybrids activate the cGAS-STING axis. Embo J 33, 2937-2946, doi: 10.15252/embj.201488726 (2014).
22. Wassermann, R. et al. Mycobacterium tuberculosis Differentially Activates cGAS- and Inflammasome-Dependent Intracellular Immune Responses through ESX-1. Cell host & microbe 17, 799-810, doi: 10.1016/j.chom.2015.05.003 (2015).
23. Das, G., Henning, D., Wright, D. & Reddy, R. Upstream regulatory elements are necessary and sufficient for transcription of a U6 RNA gene by RNA polymerase III. Embo J 7, 503-512 (1988).
24. Anders, C., Niewoehner, O., Duerst, A. & Jinek, M. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature 513, 569-573, doi: 10.1038/nature13579 (2014).
25. Nishimasu, H. et al. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 156, 935-949, doi: 10.1016/j. cell.2014.02.001 (2014).
26. Jinek, M. et al. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 343, 1247997, doi: 10.1126/science.1247997 (2014).
27. Doench, J. G. et al. Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation. Nat Biotechnol doi: 10.1038/nbt.3026 (2014).
28. Gagnon, J. A. et al. Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs. PLoS One 9, e98186, doi: 10.1371/journal.pone.0098186 (2014).
29. Brogna, S. & Wen, J. Nonsense-mediated mRNA decay (NMD) mechanisms. Nat Struct Mol Biol 16, 107-113, doi: 10.1038/nsmb.1550 (2009).
30. Cradick, T. J., Fine, E. J., Antico, C. J. & Bao, G. CRISPR/Cas9 systems targeting beta-globin and CCR5 genes have substantial off-target activity. Nucleic Acids Res 41, 9584-9592, doi: 10.1093/nar/gkt714 (2013).
31. Pattanayak, V. et al. High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat Biotechnol 31, 839-843, doi: 10.1038/nbt.2673 (2013).
32. Fu, Y. et al. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Biotechnol 31, 822-826, doi: 10.1038/nbt.2623 (2013).
33. Hsu, P. D. et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 31, 827-832, doi: 10.1038/nbt.2647 (2013).
34. Kuscu, C., Arslan, S., Singh, R., Thorpe, J. & Adli, M. Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nat Biotechnol 32, 677-683, doi: 10.1038/nbt.2916 (2014).
35. Wu, X. et al. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat Biotechnol 32, 670-676, doi: 10.1038/nbt.2889 (2014).
36. Cho, S. W. et al. Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome research 24, 132-141, doi: 10.1101/gr.162339.113 (2014).
37. Frock, R. L. et al. Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases. Nat Biotechnol 33, 179-186, doi: 10.1038/nbt.3101 (2015).
38. Tsai, S. Q. et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol 33, 187-197, doi: 10.1038/nbt.3117 (2015).
39. Veres, A. et al. Low incidence of off-target mutations in individual CRISPR-Cas9 and TALEN targeted human stem cell clones detected by whole-genome sequencing. Cell Stem Cell 15, 27-30, doi: 10.1016/j.stem.2014.04.020 (2014).
40. Smith, C. et al. Whole-genome sequencing analysis reveals high specificity of CRISPR/Cas9 and TALEN-based genome editing in human iPSCs. Cell Stem Cell 15, 12-13, doi: 10.1016/j.stem.2014.06.011 (2014).