Non-homologous DNA increases gene disruption efficiency by altering DNA repair outcomes

Nature Communications

Volumn 7, Issue , 2016, Pages

  Richardson, C D ^a   Ray, G J ^a   Bray, N L ^a   Corn, J E ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CRISPR ASSOCIATED PROTEIN; DOUBLE STRANDED DNA; ENDONUCLEASE; GUIDE RNA; RIBONUCLEOPROTEIN; SINGLE STRANDED DNA; DNA; OLIGONUCLEOTIDE;

CELLS AND CELL COMPONENTS; CYTOGENETICS; DNA; ENZYME; ENZYME ACTIVITY; GENE; GENETIC ENGINEERING; GENOME;

ALLELE; ARTICLE; CELL POPULATION; CONTROLLED STUDY; DNA REPAIR; EMBRYO; FEMALE; GENE DISRUPTION; GENE FREQUENCY; HEK293 CELL LINE; HELA CELL LINE; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; HUMAN GENOME; INDEL MUTATION; JURKAT CELL LINE; K562 CELL LINE; MOLECULAR CLONING; NON HOMOLOGOUS OLIGONUCLEOTIDE ENHANCEMENT; U2OS CELL LINE; GENE DELETION; GENE LOCUS; HOMOZYGOTE; METABOLISM; NUCLEOTIDE SEQUENCE; TUMOR CELL LINE;

BASE SEQUENCE; CELL LINE, TUMOR; CRISPR-ASSOCIATED PROTEINS; DNA; DNA REPAIR; GENE DELETION; GENETIC LOCI; HEK293 CELLS; HOMOZYGOTE; HUMANS; OLIGONUCLEOTIDES;

EID: 84983354429     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms12463     Document Type: Article

References (20)

1. Yang, L., Yang, J. L., Byrne, S., Pan, J. & Church, G. M. in Current Protocols in Molecular Biology. (eds Ausubel, Frederick M. et al.) 107, 31.1.1-31.1.17 (2014).
2. Doudna, J. A. & Charpentier, E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 346, 1258096 (2014).
3. Lin, S., Staahl, B. T., Alla, R. K. & Doudna, J. A. Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery. eLife 3, e04766 (2014).
4. Yang, L. et al. Optimization of scarless human stem cell genome editing. Nucleic Acids Res. 41, 9049-9061 (2013).
5. Ran, F. A. et al. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154, 1380-1389 (2013).
6. Kim, S., Kim, D., Cho, S. W., Kim, J. & Kim, J.-S. Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins. Genome Res. 24, 1012-1019 (2014).
7. Doench, J. G. et al. Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation. Nat. Biotechnol. 32, 1262-1267 (2014).
8. Moreno-Mateos, M. A. et al. CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat. Methods 12, 982-988 (2015).
9. Richardson, C. D., Ray, G. J., DeWitt, M. A., Curie, G. L. & Corn, J. E. Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA. Nat. Biotechnol. 34, 339-344 (2016).
10. Moore, J. K. & Haber, J. E. Capture of retrotransposon DNA at the sites of chromosomal double-strand breaks. Nature 383, 644-646 (1996).
11. Teng, S. C., Kim, B. & Gabriel, A. Retrotransposon reverse-Transcriptase-mediated repair of chromosomal breaks. Nature 383, 641-644 (1996):
12. Haviv-Chesner, A., Kobayashi, Y., Gabriel, A. & Kupiec, M. Capture of linear fragments at a double-strand break in yeast. Nucleic Acids Res. 35, 5192-5202 (2007).
13. Lin, Y. & Waldman, A. S. Promiscuous patching of broken chromosomes in mammalian cells with extrachromosomal DNA. Nucleic Acids Res. 29, 3975-3981 (2001).
14. Onozawa, M. et al. Repair of DNA double-strand breaks by templated nucleotide sequence insertions derived from distant regions of the genome. Proc. Natl Acad. Sci. 111, 7729-7734 (2014).
15. Ono, R. et al. Double strand break repair by capture of retrotransposon sequences and reverse-Transcribed spliced mRNA sequences in mouse zygotes. Sci. Rep. 5, 12281 (2015).
16. Tsai, S. Q. et al. GUIDE-seq enables genome-wide profiling of off-Target cleavage by CRISPR-Cas nucleases. Nat. Biotechnol. 33, 187-197 (2015).
17. 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 (2014).
18. Slaymaker, I. M. et al. Rationally engineered Cas9 nucleases with improved specificity. Science 351, 84-88 (2016).
19. Kleinstiver, B. P. et al. Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature 523, 481-485 (2015).
20. Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821 (2012).