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CRISPR system: Discovery, development and off-target detection
Abstract
As a revolutionary gene editing tool based on the adaptive immune defense mechanism of bacteria and archaea against exogenous DNA invasion, CRISPR/Cas system shows many remarkable characteristics over ZFNs and TALENs. However, off-target effect remains as one of the major imperfection of CRISPR/Cas system, hindering its further application in translational research. In this review, we highlight major breakthrough cross the development/application of this powerful toolkit, and summarize feasible methods for detecting potential off-target effects during genetic manipulation. We hope this review will assist scientists for accurate genomic editing in their future research.
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“The off-target effect can possibly cause harmful events such as sequence mutation, deletion, rearrangement, immune response, and oncogene activation, which limits the application of the CRISPR/Cas-9 editing system for therapeutic purposes.65”
From Mechanism and Applications of CRISPR/Cas-9-Mediated Genome Editing (2021) · cites this paper as [65]
In the citing paper
“The off-target effect can possibly cause harmful events such as sequence mutation, deletion, rearrangement, immune response, and oncogene activation, which limits the application of the CRISPR/Cas-9 editing system for therapeutic purposes.65”
From Mechanism and Applications of CRISPR/Cas-9-Mediated Genome Editing (2021) · cites this paper as [65]
Citations
Cites
Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage
Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A., & Liu, D. R. (2016) · Nature · doi:10.1038/nature17946 · Cited by 5,437
Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage
Gaudelli, N. M., Komor, A. C., Rees, H. A., Packer, M. S., Badran, A. H., Bryson, D. I., & Liu, D. R. (2017) · Nature · doi:10.1038/nature24644 · Cited by 4,184
In vivo genome editing using Staphylococcus aureus Cas9
Ran, F. A., Cong, L., Yan, W. X., Scott, D. A., Gootenberg, J. S., Kriz, A. J., Zetsche, B., Shalem, O., Wu, X., Makarova, K. S., et al. (2015) · Nature · doi:10.1038/nature14299 · Cited by 2,687
High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects
Kleinstiver, B. P., Pattanayak, V., Prew, M. S., Tsai, S. Q., Nguyen, N. T., Zheng, Z., & Joung, J. K. (2016) · Nature · doi:10.1038/nature16526 · Cited by 2,673
CRISPR RNA Maturation by Trans-Encoded Small RNA and Host Factor RNase III
Deltcheva, E., Chylinski, K., Sharma, C. M., Gonzales, K., Chao, Y., Pirzada, Z. A., Eckert, M. R., Vogel, J., & Charpentier, E. (2011) · Nature · doi:10.1038/nature09886 · Cited by 2,563
Rationally engineered Cas9 nucleases with improved specificity
Slaymaker, I. M., Gao, L., Zetsche, B., Scott, D. A., Yan, W. X., & Zhang, F. (2016) · Science · doi:10.1126/science.aad5227 · Cited by 2,414
Crystal structure of Cas9 in complex with guide RNA and target DNA
Nishimasu, H., Ran, F. A., Hsu, P. D., Konermann, S., Shehata, S. I., Dohmae, N., Ishitani, R., Zhang, F., & Nureki, O. (2014) · Cell · doi:10.1016/j.cell.2014.02.001 · Cited by 2,306
GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases
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., et al. (2015) · Nature Biotechnology · doi:10.1038/nbt.3117 · Cited by 2,268
Targeted capture and massively parallel sequencing of 12 human exomes
Ng, S. B., Turner, E. H., Robertson, P. D., Flygare, S. D., Bigham, A. W., Lee, C., Shaffer, T., Wong, M., Bhattacharjee, A., Eichler, E. E., et al. (2009) · Nature · doi:10.1038/nature08250 · Cited by 2,030
Evolved Cas9 variants with broad PAM compatibility and high DNA specificity
Hu, J. H., Miller, S. M., Geurts, M. H., Tang, W., Chen, L., Sun, N., Zeina, C. M., Gao, X., Rees, H. A., Lin, Z., et al. (2018) · Nature · doi:10.1038/nature26155 · Cited by 1,552
Flagged first, then by citations
Research works printed but not linked: 47
- Ishino, 1987, Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product, J. Bacteriol., 169, 5429, 10.1128/jb.169.12.5429-5433.1987 · DOI · Paper page
- Mojica, 1995, Long stretches of short tandem repeats are present in the largest replicons of the archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning, Mol. Microbiol., 17, 85, 10.1111/j.1365-2958.1995.mmi_17010085.x · DOI
- Nakata, 1989, Unusual nucleotide arrangement with repeated sequences in the Escherichia coli K-12 chromosome, J. Bacteriol., 171, 3553, 10.1128/jb.171.6.3553-3556.1989 · DOI
- Mojica, 2000, Biological significance of a family of regularly spaced repeats in the genomes of archaea, bacteria and mitochondria, Mol. Microbiol., 36, 244, 10.1046/j.1365-2958.2000.01838.x · DOI
- Jansen, 2002, Identification of genes that are associated with DNA repeats in prokaryotes, Mol. Microbiol., 43, 1565, 10.1046/j.1365-2958.2002.02839.x · DOI · Paper page
- Bolotin, 2005, Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin, Microbiology, 151, 2551, 10.1099/mic.0.28048-0 · DOI · Paper page
- Mojica, 2005, Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements, J. Mol. Evol., 60, 174, 10.1007/s00239-004-0046-3 · DOI · Paper page
- Barrangou, 2007, CRISPR provides acquired resistance against viruses in prokaryotes, Science, 315, 1709, 10.1126/science.1138140 · DOI · Paper page
- Marraffini, 2008, CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA, Science, 322, 1843, 10.1126/science.1165771 · DOI · Paper page
- Garneau, 2010, The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA, Nature, 468, 67, 10.1038/nature09523 · DOI
- Jinek, 2012, A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity, Science, 337, 816, 10.1126/science.1225829 · DOI · Paper page
- Gaj, 2013, ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering, Trends Biotechnol., 31, 397, 10.1016/j.tibtech.2013.04.004 · DOI · Paper page
- Mali, 2013, RNA-guided human genome engineering via Cas9, Science, 339, 823, 10.1126/science.1232033 · DOI · Paper page
- Cong, 2013, Multiplex genome engineering using CRISPR/Cas systems, Science, 339, 819, 10.1126/science.1231143 · DOI · Paper page
- Makarova, 2011, Evolution and classification of the CRISPR-Cas systems, Nat. Rev. Microbiol., 9, 467, 10.1038/nrmicro2577 · DOI · Paper page
- Carr, 2009, Genome engineering, Nat. Biotechnol., 27, 1151, 10.1038/nbt.1590 · DOI
- Anders, 2014, Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease, Nature, 513, 569, 10.1038/nature13579 · DOI · Paper page
- Kleinstiver, 2015, Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition, Nat. Biotechnol., 33, 1293, 10.1038/nbt.3404 · DOI · Paper page
- Xie, 2018, SaCas9 requires 5’-NNGRRT-3’ PAM for sufficient cleavage and possesses higher cleavage activity than SpCas9 or FnCpf1 in human cells, Biotechnol. J., 13, 10.1002/biot.201800080 · DOI
- Price, 2015, Cas9-mediated targeting of viral RNA in eukaryotic cells, Proc. Natl. Acad. Sci. U. S. A., 112, 6164, 10.1073/pnas.1422340112 · DOI
- Lee, 2016, The Neisseria meningitidis CRISPR-Cas9 system enables specific genome editing in mammalian cells, Mol. Ther., 24, 645, 10.1038/mt.2016.8 · DOI
- Wang, 2019, Optimized CRISPR guide RNA design for two high-fidelity Cas9 variants by deep learning, Nat. Commun., 10, 4284, 10.1038/s41467-019-12281-8 · DOI · Paper page
- Zetsche, 2015, Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system, Cell, 163, 759, 10.1016/j.cell.2015.09.038 · DOI · Paper page
- Yang, 2016, PAM-dependent target DNA recognition and cleavage by C2c1 CRISPR-Cas endonuclease, Cell, 167
- Teng, 2018, Repurposing CRISPR-Cas12b for mammalian genome engineering, Cell Discov., 4, 63, 10.1038/s41421-018-0069-3 · DOI
- Strecker, 2019, Engineering of CRISPR-Cas12b for human genome editing, Nat. Commun., 10, 212, 10.1038/s41467-018-08224-4 · DOI
- Abudayyeh, 2016, C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector, Science, 353, 10.1126/science.aaf5573 · DOI · Paper page
- East-Seletsky, 2016, Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection, Nature, 538, 270, 10.1038/nature19802 · DOI · Paper page
- Gootenberg, 2017, Nucleic acid detection with CRISPR-Cas13a/C2c2, Science, 356, 438, 10.1126/science.aam9321 · DOI
- Gootenberg, 2018, Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6, Science, 360, 439, 10.1126/science.aaq0179 · DOI
- Smargon, 2017, Cas13b is a type VI-B CRISPR-associated RNA-guided RNase differentially regulated by accessory proteins Csx27 and Csx28, Mol. Cell, 65
- Konermann, 2018, Transcriptome engineering with RNA-targeting type VI-D CRISPR effectors, Cell, 173
- Freije, 2019, Programmable inhibition and detection of RNA viruses using Cas13, Mol. Cell, 76
- Yang, 2019, Dynamic imaging of RNA in living cells by CRISPR-Cas13 systems, Mol. Cell, 76
- Harrington, 2018, Programmed DNA destruction by miniature CRISPR-Cas14 enzymes, Science, 362, 839, 10.1126/science.aav4294 · DOI
- Oakes, 2019, CRISPR-Cas9 circular permutants as programmable scaffolds for genome modification, Cell, 176
- Anzalone, 2019, Search-and-replace genome editing without double-strand breaks or donor DNA, Nature, 576, 149, 10.1038/s41586-019-1711-4 · DOI · Paper page
- Chang, 2017, Non-homologous DNA end joining and alternative pathways to double-strand break repair, Nat. Rev. Mol. Cell Biol., 18, 495, 10.1038/nrm.2017.48 · DOI · Paper page
- Mashal, 1995, Detection of mutations by cleavage of DNA heteroduplexes with bacteriophage resolvases, Nat. Genet., 9, 177, 10.1038/ng0295-177 · DOI
- Bae, 2014, Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases, Bioinformatics, 30, 1473, 10.1093/bioinformatics/btu048 · DOI · Paper page
- Li, 2019, Whole genome sequencing reveals rare off-target mutations and considerable inherent genetic or/and somaclonal variations in CRISPR/Cas9-edited cotton plants, Plant Biotechnol. J., 17, 858, 10.1111/pbi.13020 · DOI
- Solomon, 1988, Mapping proteinDNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene, Cell, 53, 937, 10.1016/S0092-8674(88)90469-2 · DOI
- Crosetto, 2013, Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing, Nat. Methods, 10, 361, 10.1038/nmeth.2408 · DOI · Paper page
- Gabriel, 2011, An unbiased genome-wide analysis of zinc-finger nuclease specificity, Nat. Biotechnol., 29, 816, 10.1038/nbt.1948 · DOI · Paper page
- Hu, 2016, Detecting DNA double-stranded breaks in mammalian genomes by linear amplification–mediated high-throughput genome-wide translocation sequencing, Nat. Protoc., 11, 853, 10.1038/nprot.2016.043 · DOI
- Roukos, 2013, Spatial dynamics of chromosome translocations in living cells, Science, 341, 660, 10.1126/science.1237150 · DOI
- Kim, 2015, Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells, Nat. Methods, 12, 237, 10.1038/nmeth.3284 · DOI · Paper page
Cited by
Sorted by citations
Mechanism and Applications of CRISPR/Cas-9-Mediated Genome Editing
Mengstie, M. A., & Wondimu, B. Z. (2021) · Biologics: Targets and Therapy · doi:10.2147/btt.s326422 · Cited by 478
Metadata
- Authors
- Chen, S., Yao, Y., Zhang, Y., & Fan, G.
- Venue
- Cellular Signalling
- Publisher
- Elsevier BV
- Published
- 2020-06
- Volume
- 70
- Pages
- 109577
- ISSN
- 0898-6568
- Cited by
- 60
- References
- 20
- Language
- en
- Licence
- Funders
- National Natural Science Foundation of China (31872831)
- Ministry of Science and Technology of the People's Republic of China (2018YFC1004603)
- ShanghaiTech University
- Science and Technology Commission of Shanghai Municipality (19JC1413800)
- Shanghai Shuguang Program (19SG55)
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