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Volumn 38, Issue 6, 2015, Pages 475-481

Measuring and reducing off-target activities of programmable nucleases including CRISPR-Cas9

Author keywords

[No Author keywords available]

Indexed keywords

CRISPR ASSOCIATED PROTEIN; CRISPR ASSOCIATED PROTEIN 9; NUCLEASE; UNCLASSIFIED DRUG; ENDONUCLEASE;

EID: 84938739634     PISSN: 10168478     EISSN: 02191032     Source Type: Journal    
DOI: 10.14348/molcells.2015.0103     Document Type: Review
Times cited : (165)

References (57)
  • 1
    • 84896308706 scopus 로고    scopus 로고
    • Cas-OFFinder: A fast andversatile algorithm that searches for potential off-target sites ofCas9 RNA-guided endonucleases
    • Bae, S., Park, J., and Kim, J.S. (2014). Cas-OFFinder: A fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 30, 1473-1475.
    • (2014) Bioinformatics , vol.30 , pp. 1473-1475
    • Bae, S.1    Park, J.2    Kim, J.S.3
  • 2
    • 0037510038 scopus 로고    scopus 로고
    • Enhancing gene targeting with designed zinc finger nucleases
    • Bibikova, M., Beumer, K., Trautman, J.K., and Carroll, D. (2003). Enhancing gene targeting with designed zinc finger nucleases. Science 300, 764.
    • (2003) Science , vol.300 , pp. 764
    • Bibikova, M.1    Beumer, K.2    Trautman, J.K.3    Carroll, D.4
  • 6
    • 84874624936 scopus 로고    scopus 로고
    • Targetedgenome engineering in human cells with the Cas9 RNA-guided endonuclease
    • Cho, S.W., Kim, S., Kim, J.M., and Kim, J.S. (2013a). Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat. Biotechnol. 31, 230-232.
    • (2013) Nat. Biotechnol , vol.31 , pp. 230-232
    • Cho, S.W.1    Kim, S.2    Kim, J.M.3    Kim, J.S.4
  • 7
    • 84884911076 scopus 로고    scopus 로고
    • Heritable gene knockout in Caenorhabditis elegans by directinjectionofCas9-sgRNAribonucleoproteins
    • Cho, S.W., Lee, J., Carroll, D., Kim, J.S., and Lee, J. (2013b). Heritable gene knockout in Caenorhabditis elegans by direct injection of Cas9-sgRNA ribonucleoproteins. Genetics 195, 1177-1180.
    • (2013) Genetics , vol.195 , pp. 1177-1180
    • Cho, S.W.1    Lee, J.2    Carroll, D.3    Kim, J.S.4    Lee, J.5
  • 8
    • 84891710947 scopus 로고    scopus 로고
    • Analysisofoff-targeteffectsofCRISPR/Cas-derived RNA-guided endonucleases and nickases
    • Cho, S.W., Kim, S., Kim, Y., Kweon, J., Kim, H.S., Bae, S., and Kim, J.S. (2014). Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res. 24, 132-141.
    • (2014) Genome Res , vol.24 , pp. 132-141
    • Cho, S.W.1    Kim, S.2    Kim, Y.3    Kweon, J.4    Kim, H.S.5    Bae, S.6    Kim, J.S.7
  • 10
    • 84884950106 scopus 로고    scopus 로고
    • CRISPR/as9systemstargetingbeta-globinandCCR5geneshavesubstantial off-target activity
    • Cradick, T.J., Fine, E.J., Antico, C.J., and Bao, G. (2013) CRISPR/ as9 systems targeting beta-globin and CCR5 genes have substantial off-target activity. Nucleic Acids Res. 41, 9584-9592.
    • (2013) Nucleic Acids Res , vol.41 , pp. 9584-9592
    • Cradick, T.J.1    Fine, E.J.2    Antico, C.J.3    Bao, G.4
  • 12
    • 84923275611 scopus 로고    scopus 로고
    • Genome-wide detection of DNA double-stranded breaksinduced by engineered nucleases. Nat
    • Frock, R.L., Hu, J., Meyers, R.M., Ho, Y.J., Kii, E., and Alt, F.W. (2015). Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases. Nat. Biotechnol. 33, 179-186.
    • (2015) Biotechnol , vol.33 , pp. 179-186
    • Frock, R.L.1    Hu, J.2    Meyers, R.M.3    Ho, Y.J.4    Kii, E.5    Alt, F.W.6
  • 13
    • 84880570576 scopus 로고    scopus 로고
    • High-frequencyoff-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat
    • Fu, Y., Foden, J.A., Khayter, C., Maeder, M.L., Reyon, D., Joung, J.K., and Sander, J.D. (2013). High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat. Biotechnol. 31, 822-826.
    • (2013) Biotechnol , vol.31 , pp. 822-826
    • Fu, Y.1    Foden, J.A.2    Khayter, C.3    Maeder, M.L.4    Reyon, D.5    Joung, J.K.6    Sander, J.D.7
  • 14
    • 84896929630 scopus 로고    scopus 로고
    • ImprovingCRISPR-Casnucleasespecificityusingtruncated guide RNAs
    • 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.
    • (2014) Nat. Biotechnol , vol.32 , pp. 279-284
    • Fu, Y.1    Sander, J.D.2    Reyon, D.3    Cascio, V.M.4    Joung, J.K.5
  • 18
    • 84865070369 scopus 로고    scopus 로고
    • A programmable dual-RNA-guided DNAendonuclease in adaptive bacterial immunity
    • 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.
    • (2012) Science , vol.337 , pp. 816-821
    • Jinek, M.1    Chylinski, K.2    Fonfara, I.3    Hauer, M.4    Doudna, J.A.5    Charpentier, E.6
  • 20
    • 84898778301 scopus 로고    scopus 로고
    • A guide to genome engineering withprogrammable nucleases.
    • Kim, H., and Kim, J.S. (2014). A guide to genome engineering with programmable nucleases. Nat. Rev. Genet. 15, 321-334.
    • (2014) Nat. Rev. Genet , vol.15 , pp. 321-334
    • Kim, H.1    Kim, J.S.2
  • 21
    • 0030032063 scopus 로고    scopus 로고
    • Hybridrestriction enzymes: Zinc finger fusions to Fok I cleavage domain
    • Kim, Y.G., Cha, J., and Chandrasegaran, S. (1996). Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc. Natl. Acad. Sci. USA 93, 1156-1160.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 1156-1160
    • Kim, Y.G.1    Cha, J.2    Chandrasegaran, S.3
  • 22
    • 67650045497 scopus 로고    scopus 로고
    • Targetedgenomeeditinginhumancellswithzincfingernucleases constructed via modular assembly
    • Kim, H.J., Lee, H.J., Kim, H., Cho, S.W., and Kim, J.S. (2009). Targeted genome editing in human cells with zinc fingernucleases constructed via modular assembly. Genome Res. 19 1279-1288.
    • (2009) Genome Res , vol.19 , pp. 1279-1288
    • Kim, H.J.1    Lee, H.J.2    Kim, H.3    Cho, S.W.4    Kim, J.S.5
  • 23
    • 77449139581 scopus 로고    scopus 로고
    • Genome editing withmodularly assembled zinc-finger nucleases
    • author reply
    • Kim, J.S., Lee, H.J., and Carroll, D. (2010). Genome editing with modularly assembled zinc-finger nucleases. Nat. Methods 7, 91;author reply 91-92.
    • (2010) Nat. Methods , vol.7 , Issue.91 , pp. 91-92
    • Kim, J.S.1    Lee, H.J.2    Carroll, D.3
  • 24
    • 80255134581 scopus 로고    scopus 로고
    • Surrogatereportersforenrichmentofcellswithnuclease-induced mutations
    • Kim, H., Um, E., Cho, S.R., Jung, C., and Kim, J.S. (2011). Surrogate reporters for enrichment of cells with nuclease-induced mutations. Nat. Methods 8, 941-943.
    • (2011) Nat. Methods , vol.8 , pp. 941-943
    • Kim, H.1    Um, E.2    Cho, S.R.3    Jung, C.4    Kim, J.S.5
  • 25
    • 84861990434 scopus 로고    scopus 로고
    • PrecisiongenomeengineeringwithprogrammableDNA-nicking enzymes
    • Kim, E., Kim, S., Kim, D.H., Choi, B.S., Choi, I.Y., and Kim, J.S. (2012). Precision genome engineering with programmable DNA-nicking enzymes. Genome Res. 22, 1327-1333.
    • (2012) Genome Res , vol.22 , pp. 1327-1333
    • Kim, E.1    Kim, S.2    Kim, D.H.3    Choi, B.S.4    Choi, I.Y.5    Kim, J.S.6
  • 27
    • 84874663256 scopus 로고    scopus 로고
    • TALENs and ZFNs areassociated with different mutation signatures
    • Kim, Y., Kweon, J., and Kim, J.S. (2013b). TALENs and ZFNs are associated with different mutation signatures. Nat. Methods 10, 185.
    • (2013) Nat. Methods , vol.10 , pp. 185
    • Kim, Y.1    Kweon, J.2    Kim, J.S.3
  • 29
    • 84892897176 scopus 로고    scopus 로고
    • Genotyping withCRISPR-Cas-derivedRNA-guidedendonucleases
    • Kim, J.M., Kim, D., Kim, S., and Kim, J.S. (2014a). Genotyping with CRISPR-Cas-derived RNA-guided endonucleases. Nat. Commun. 5, 3157.
    • (2014) Nat.Commun , vol.5 , pp. 3157
    • Kim, J.M.1    Kim, D.2    Kim, S.3    Kim, J.S.4
  • 30
    • 84901834420 scopus 로고    scopus 로고
    • Highlyefficient RNA-guided genome editing in human cells via deliveryof purified Cas9 ribonucleoproteins
    • Kim, S., Kim, D., Cho, S.W., Kim, J., and Kim, J.S. (2014b). Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins. Genome Res. 24, 1012-1019.
    • (2014) Genome Res , vol.24 , pp. 1012-1019
    • Kim, S.1    Kim, D.2    Cho, S.W.3    Kim, J.4    Kim, J.S.5
  • 31
    • 84923846574 scopus 로고    scopus 로고
    • Digenome-seq: Genome-wideprofiling of CRISPR-Cas9 off-target effects in human cells
    • Kim, D., Bae, S., Park, J., Kim, E., Kim, S., Yu, H.R., Hwang, J., Kim, J.I. and Kim, J.S. (2015). Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells. Nat. Methods 12, 237-243.
    • (2015) Nat. Methods , vol.12 , pp. 237-243
    • Kim, D.1    Bae, S.2    Park, J.3    Kim, E.4    Kim, S.5    Yu, H.R.6    Hwang, J.7    Kim, J.I.8    Kim, J.S.9
  • 32
    • 84903545084 scopus 로고    scopus 로고
    • Genome-wide analysis reveals characteristics of off-target sitesbound by the Cas9 endonuclease
    • Kuscu, C., Arslan, S., Singh, R., Thorpe, J., and Adli, M. (2014). Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nat. Biotechnol. 32, 677-683.
    • (2014) Nat. Biotechnol , vol.32 , pp. 677-683
    • Kuscu, C.1    Arslan, S.2    Singh, R.3    Thorpe, J.4    Adli, M.5
  • 33
    • 74949133880 scopus 로고    scopus 로고
    • Targeted chromosomaldeletions in human cells using zinc finger nucleases
    • Lee, H.J., Kim, E., and Kim, J.S. (2010). Targeted chromosomal deletions in human cells using zinc finger nucleases. Genome Res. 20, 81-89.
    • (2010) Genome Res , vol.20 , pp. 81-89
    • Lee, H.J.1    Kim, E.2    Kim, J.S.3
  • 34
    • 84863275797 scopus 로고    scopus 로고
    • Targetedchromosomal duplications and inversions in the human genomeusing zinc finger nucleases
    • Lee, H.J., Kweon, J., Kim, E., Kim, S. and Kim, J.S. (2012).Targeted chromosomal duplications and inversions in the human genome using zinc finger nucleases. Genome Res. 22, 539-548.
    • (2012) Genome Res , vol.22 , pp. 539-548
    • Lee, H.J.1    Kweon, J.2    Kim, E.3    Kim, S.4    Kim, J.S.5
  • 36
    • 84884160273 scopus 로고    scopus 로고
    • CAS9transcriptional activators for target specificity screening and pairednickasesforcooperativegenomeengineering
    • Mali, P., Aach, J., Stranges, P.B., Esvelt, K.M., Moosburner, M., Kosuri, S., Yang, L. and Church, G.M. (2013a). CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat. Biotechnol. 31, 833-838.
    • (2013) Nat. Biotechnol , vol.31 , pp. 833-838
    • Mali, P.1    Aach, J.2    Stranges, P.B.3    Esvelt, K.M.4    Moosburner, M.5    Kosuri, S.6    Yang, L.7    Church, G.M.8
  • 39
    • 72149090954 scopus 로고    scopus 로고
    • Asimpleciphergoverns DNA recognition by TAL effectors
    • Moscou, M.J., and Bogdanove, A.J. (2009). A simple cipher governs DNA recognition by TAL effectors. Science 326, 1501.
    • (2009) Science , vol.326 , pp. 1501
    • Moscou, M.J.1    Bogdanove, A.J.2
  • 40
    • 80053039555 scopus 로고    scopus 로고
    • A novel TALE nuclease scaffoldenables high genome editing activity in combination with low toxicity
    • Mussolino, C., Morbitzer, R., Lutge, F., Dannemann, N., Lahaye, T. and Cathomen, T. (2011). A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity. Nucleic Acids Res. 39, 9283-9293.
    • (2011) Nucleic Acids Res , vol.39 , pp. 9283-9293
    • Mussolino, C.1    Morbitzer, R.2    Lutge, F.3    Dannemann, N.4    Lahaye, T.5    Cathomen, T.6
  • 41
    • 70949104150 scopus 로고    scopus 로고
    • A rapid and efficient method of genotyping zebrafishmutants
    • Parant, J.M., George, S.A., Pryor, R., Wittwer, C.T., and Yost, H.J. (2009). A rapid and efficient method of genotyping zebrafish mutants. Dev. Dyn. 238, 3168-3174.
    • (2009) Dev. Dyn , vol.238 , pp. 3168-3174
    • Parant, J.M.1    George, S.A.2    Pryor, R.3    Wittwer, C.T.4    Yost, H.J.5
  • 43
    • 80052293623 scopus 로고    scopus 로고
    • Revealingoff-targetcleavagespecificitiesofzinc-fingernucleases by in vitro selection
    • Pattanayak, V., Ramirez, C.L., Joung, J.K., and Liu, D.R. (2011). Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection. Nat. Methods 8, 765-770.
    • (2011) Nat. Methods , vol.8 , pp. 765-770
    • Pattanayak, V.1    Ramirez, C.L.2    Joung, J.K.3    Liu, D.R.4
  • 44
    • 84884155038 scopus 로고    scopus 로고
    • High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity
    • Pattanayak, V., Lin, S., Guilinger, J.P., Ma, E., Doudna, J.A., and Liu, D.R. (2013). High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat. Biotechnol. 31, 839-843.
    • (2013) Nat. Biotechnol , vol.31 , pp. 839-843
    • Pattanayak, V.1    Lin, S.2    Guilinger, J.P.3    Ma, E.4    Doudna, J.A.5    Liu, D.R.6
  • 45
    • 84901843996 scopus 로고    scopus 로고
    • Gene disruption by cell-penetratingpeptide-mediated delivery of Cas9 protein and guide RNA
    • Ramakrishna, S., Kwaku Dad, A.B., Beloor, J., Gopalappa, R., Lee, S.K., and Kim, H. (2014). Gene disruption by cell-penetrating peptide-mediated delivery of Cas9 protein and guide RNA. Genome Res. 24, 1020-1027.
    • (2014) Genome Res , vol.24 , pp. 1020-1027
    • Ramakrishna, S.1    Kwaku Dad, A.B.2    Beloor, J.3    Gopalappa, R.4    Lee, S.K.5    Kim, H.6
  • 48
    • 84903943282 scopus 로고    scopus 로고
    • Whole-genome sequencing analysis reveals high specificity of CRISPR/Cas9 and TALEN-based genome editing in human iPSCs
    • Smith, C., Gore, A., Yan, W., Abalde-Atristain, L., Li, Z., He, C., Wang, Y., Brodsky, R.A., Zhang, K., Cheng, L., et al. (2014). Whole-genome sequencing analysis reveals high specificity of CRISPR/Cas9 and TALEN-based genome editing in human iPSCs. Cell Stem Cell 15, 12-13.
    • (2014) Cell Stem Cell , vol.15 , pp. 12-13
    • Smith, C.1    Gore, A.2    Yan, W.3    Abalde-Atristain, L.4    Li, Z.5    He, C.6    Wang, Y.7    Brodsky, R.A.8    Zhang, K.9    Cheng, L.10
  • 52
    • 84904010334 scopus 로고    scopus 로고
    • Low incidence of off-target mutations inindividual CRISPR-Cas9 and TALEN targeted human stem cellclones detected by whole-genome sequencing
    • Veres, A., Gosis, B.S., Ding, Q., Collins, R., Ragavendran, A., Brand, H., Erdin, S., Cowan, C.A., Talkowski, M.E., and Musunuru, K. (2014). 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.
    • (2014) Cell Stem Cell , vol.15 , pp. 27-30
    • Veres, A.1    Gosis, B.S.2    Ding, Q.3    Collins, R.4    Ragavendran, A.5    Brand, H.6    Erdin, S.7    Cowan, C.A.8    Talkowski, M.E.9    Musunuru, K.10
  • 53
    • 84924666891 scopus 로고    scopus 로고
    • Comparison of T7E1and surveyor mismatch cleavage assays to detect mutationstriggered by engineered nucleases
    • Vouillot, L., Thelie, A., and Pollet, N. (2015). Comparison of T7E1 and surveyor mismatch cleavage assays to detect mutations triggered by engineered nucleases. G3 (Bethesda) 5, 407-415.
    • (2015) G3 (Bethesda) , vol.5 , pp. 407-415
    • Vouillot, L.1    Thelie, A.2    Pollet, N.3
  • 56
    • 84923229919 scopus 로고    scopus 로고
    • An efficient genotyping methodforgenome-modifiedanimalsandhumancells generated with CRISPR/Cas9 system
    • Zhu, X., Xu, Y., Yu, S., Lu, L., Ding, M., Cheng, J., Song, G., Gao, X., Yao, L., Fan, D., et al. (2014). An efficient genotyping method for genome-modified animals and human cells generated with CRISPR/Cas9 system. Sci. Rep. 4, 6420.
    • (2014) Sci. Rep , vol.4 , pp. 6420
    • Zhu, X.1    Xu, Y.2    Yu, S.3    Lu, L.4    Ding, M.5    Cheng, J.6    Song, G.7    Gao, X.8    Yao, L.9    Fan, D.10


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.