Login Register Cart 0
Generic placeholder image

Current Bioinformatics

Editor-in-Chief

ISSN (Print): 1574-8936
ISSN (Online): 2212-392X

Back
Journal Home About Journal Editorial Board Journal Insight Current Issue Volumes/Issues
Subscribe
Review Article

CRISPR/ Cas9 Off-targets: Computational Analysis of Causes, Prediction, Detection, and Overcoming Strategies

Author(s): Roshan Kumar Roy, Ipsita Debashree, Sonal Srivastava, Narayan Rishi and Ashish Srivastava*

Volume 17, Issue 2, 2022

Published on: 08 July, 2021

Page: [119 - 132] Pages: 14

DOI: 10.2174/1574893616666210708150439

Price: $65

Abstract

CRISPR/Cas9 technology is a highly flexible RNA-guided endonuclease (RGEN) based gene-editing tool that has transformed the field of genomics, gene therapy, and genome/ epigenome imaging. Its wide range of applications provides immense scope for understanding as well as manipulating genetic/epigenetic elements. However, the RGEN is prone to off-target mutagenesis that leads to deleterious effects. This review details the molecular and cellular mechanisms underlying the off-target activity, various available detection tools and prediction methodology ranging from sequencing to machine learning approaches, and the strategies to overcome/minimise off-targets. A coherent and concise method increasing target precision would prove indispensable to concrete manipulation and interpretation of genome editing results that can revolutionise therapeutics, including clarity in genome regulatory mechanisms during development.

Keywords: Genome-wide association study, chemical genetics, drug mode of action, pathogenesis, transcriptional regulation., CRISPR/Cas9.

Next »
Graphical Abstract

[1]
Srivastava S, Upadhyay DJ, Srivastava A. Next-generation molecular diagnostics development by crispr/cas tool: Rapid detection and surveillance of viral disease outbreaks. Front Mol Biosci 2020; 7: 582499.
[2]
Kleinstiver BP, Pattanayak V, Prew MS, et al. High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Nature 2016; 529(7587): 490-5.
[http://dx.doi.org/10.1038/nature16526] [PMID: 26735016]
[3]
Sansbury BM, Hewes AM, Kmiec EB. Understanding the diversity of genetic outcomes from CRISPR-Cas generated homology-directed repair. Commun Biol 2019; 2: 458.
[http://dx.doi.org/10.1038/s42003-019-0705-y] [PMID: 31840103]
[4]
Zhu S, Li W, Liu J, et al. Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR-Cas9 library. Nat Biotechnol 2016; 34(12): 1279-86.
[http://dx.doi.org/10.1038/nbt.3715] [PMID: 27798563]
[5]
Choi PS, Meyerson M. Targeted genomic rearrangements using CRISPR/Cas technology. Nat Commun 2014; 5: 3728.
[http://dx.doi.org/10.1038/ncomms4728] [PMID: 24759083]
[6]
Cámara E, Lenitz I, Nygård Y. A CRISPR activation and interference toolkit for industrial Saccharomyces cerevisiae strain KE6-12. Sci Rep 2020; 10(1): 14605.
[http://dx.doi.org/10.1038/s41598-020-71648-w] [PMID: 32884066]
[7]
Qi LS, Larson MH, Gilbert LA, et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 2013; 152(5): 1173-83.
[http://dx.doi.org/10.1016/j.cell.2013.02.022] [PMID: 23452860]
[8]
Perez-Pinera P, Kocak DD, Vockley CM, et al. RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat Methods 2013; 10(10): 973-6.
[http://dx.doi.org/10.1038/nmeth.2600] [PMID: 23892895]
[9]
Syding LA, Nickl P, Kasparek P, Sedlacek R. CRISPR/Cas9 epigenome editing potential for rare imprinting diseases: A review. Cells 2020; 9(4): 993.
[http://dx.doi.org/10.3390/cells9040993] [PMID: 32316223]
[10]
Kalhor R, Mali P, Church GM. Rapidly evolving homing CRISPR barcodes. Nat Methods 2017; 14(2): 195-200.
[http://dx.doi.org/10.1038/nmeth.4108] [PMID: 27918539]
[11]
Tang W, Liu DR. Rewritable multi-event analog recording in bacterial and mammalian cells. Science 2018; 360(6385): eaap8992.
[12]
Xie S, Duan J, Li B, Zhou P, Hon GC. Multiplexed engineering and analysis of combinatorial enhancer activity in single cells. Mol Cell 2017; 66(2): 285-99.e5.
[http://dx.doi.org/10.1016/j.molcel.2017.03.007] [PMID: 28416141]
[13]
Schumann K, Lin S, Boyer E, et al. Generation of knock-in primary human T cells using Cas9 ribonucleoproteins. Proc Natl Acad Sci USA 2015; 112(33): 10437-42.
[http://dx.doi.org/10.1073/pnas.1512503112] [PMID: 26216948]
[14]
Fujita T, Yuno M, Fujii H. Allele-specific locus binding and genome editing by CRISPR at the p16INK4a locus. Sci Rep 2016; 6: 30485.
[http://dx.doi.org/10.1038/srep30485] [PMID: 27465215]
[15]
Chen B, Gilbert LA, Cimini BA, et al. Dynamic imaging of genomic loci in living human cells by an optimized crispr/cas system. Cell 2013; 155(2013): 1479-91.
[16]
Yu W, Mookherjee S, Chaitankar V, et al. Nrl knockdown by AAV-delivered CRISPR/Cas9 prevents retinal degeneration in mice. Nat Commun 2017; 8: 14716.
[http://dx.doi.org/10.1038/ncomms14716] [PMID: 28291770]
[17]
Cameron P, Fuller CK, Donohoue PD, et al. Mapping the genomic landscape of CRISPR-Cas9 cleavage. Nat Methods 2017; 14(6): 600-6.
[http://dx.doi.org/10.1038/nmeth.4284] [PMID: 28459459]
[18]
Xiang G, Zhang X, An C, Cheng C, Wang H. Temperature effect on CRISPR-Cas9 mediated genome editing. J Genet Genomics 2017; 44(4): 199-205.
[http://dx.doi.org/10.1016/j.jgg.2017.03.004] [PMID: 28412228]
[19]
Kim Y, Kweon J, Kim A, et al. A library of TAL effector nucleases spanning the human genome. Nat Biotechnol 2013; 31(3): 251-8.
[http://dx.doi.org/10.1038/nbt.2517] [PMID: 23417094]
[20]
Lee HJ, Kweon J, Kim E, Kim S, Kim J-S. Targeted chromosomal duplications and inversions in the human genome using zinc finger nucleases. Genome Res 2012; 22(3): 539-48.
[http://dx.doi.org/10.1101/gr.129635.111] [PMID: 22183967]
[21]
Kumar P, Malik YS, Ganesh B, et al. CRISPR-Cas system: An approach with potentials for COVID-19 diagnosis and therapeutics. Front Cell Infect Microbiol 2020; 10: 576875.
[http://dx.doi.org/10.3389/fcimb.2020.576875] [PMID: 33251158]
[22]
Zhang F, Abudayyeh OO, Gootenberg JS, Sciences C, Mathers L. A protocol for detection of COVID-19 using CRISPR diagnostics Bioarchive. 2020; 1-8.
[23]
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 2014; 32(7): 677-83.
[http://dx.doi.org/10.1038/nbt.2916] [PMID: 24837660]
[24]
Fu Y, Sander JD, Reyon D, Cascio VM, Joung JK. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol 2014; 32(3): 279-84.
[http://dx.doi.org/10.1038/nbt.2808] [PMID: 24463574]
[25]
Palermo G, Ricci CG, Fernando A, et al. Protospacer adjacent motif-induced allostery activates CRISPR-Cas9. J Am Chem Soc 2017; 139(45): 16028-31.
[http://dx.doi.org/10.1021/jacs.7b05313] [PMID: 28764328]
[26]
Boyle EA, Andreasson JOL, Chircus LM, et al. High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding. Proc Natl Acad Sci USA 2017; 114(21): 5461-6.
[http://dx.doi.org/10.1073/pnas.1700557114] [PMID: 28495970]
[27]
Palermo G. Structure and dynamics of the CRISPR-Cas9 catalytic complex. J Chem Inf Model 2019; 59(5): 2394-406.
[http://dx.doi.org/10.1021/acs.jcim.8b00988] [PMID: 30763088]
[28]
Ricci CG, Chen JS, Miao Y, et al. Deciphering off-target effects in CRISPR-cas9 through accelerated molecular dynamics. ACS Cent Sci 2019; 5(4): 651-62.
[http://dx.doi.org/10.1021/acscentsci.9b00020] [PMID: 31041385]
[29]
Szczelkun MD, Tikhomirova MS, Sinkunas T, et al. Direct observation of R-loop formation by single RNA-guided Cas9 and cascade effector complexes. Proc Natl Acad Sci USA 2014; 111(27): 9798-803.
[http://dx.doi.org/10.1073/pnas.1402597111] [PMID: 24912165]
[30]
Xue C, Whitis NR, Sashital DG. Conformational control of cascade interference and priming activities in crispr immunity. Mol Cell 2016; 64(4): 826-34.
[http://dx.doi.org/10.1016/j.molcel.2016.09.033] [PMID: 27871367]
[31]
Chen JS, Dagdas YS, Kleinstiver BP, et al. Enhanced proofreading governs CRISPR-Cas9 targeting accuracy. Nature 2017; 550(7676): 407-10.
[http://dx.doi.org/10.1038/nature24268] [PMID: 28931002]
[32]
Raper AT, Stephenson AA, Suo Z. Functional insights revealed by the kinetic mechanism of CRISPR/Cas9. J Am Chem Soc 2018; 140(8): 2971-84.
[http://dx.doi.org/10.1021/jacs.7b13047] [PMID: 29442507]
[33]
Liu H, Ding Y, Zhou Y, Jin W, Xie K, Chen L-L. CRISPR-P 2.0: An improved crispr-cas9 tool for genome editing in plants. Mol Plant 2017; 10(3): 530-2.
[http://dx.doi.org/10.1016/j.molp.2017.01.003] [PMID: 28089950]
[34]
Klein M, Eslami-Mossallam B, Arroyo DG, Depken M. Hybridization kinetics explains CRISPR-Cas off-targeting rules. Cell Rep 2018; 22(6): 1413-23.
[http://dx.doi.org/10.1016/j.celrep.2018.01.045] [PMID: 29425498]
[35]
Newton MD, Taylor BJ, Driessen RPC, et al. DNA stretching induces Cas9 off-target activity. Nat Struct Mol Biol 2019; 26(3): 185-92.
[http://dx.doi.org/10.1038/s41594-019-0188-z] [PMID: 30804513]
[36]
Fu Y, Foden JA, Khayter C, et al. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Biotechnol 2013; 31(9): 822-6.
[http://dx.doi.org/10.1038/nbt.2623] [PMID: 23792628]
[37]
Richardson CD, Ray GJ, DeWitt MA, Curie GL, Corn JE. Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA. Nat Biotechnol 2016; 34(3): 339-44.
[http://dx.doi.org/10.1038/nbt.3481] [PMID: 26789497]
[38]
Bowden AR, Morales-Juarez DA, Sczaniecka-Clift M, et al. Parallel CRISPR-Cas9 screens clarify impacts of p53 on screen performance. eLife 2020; 9: e55325.
[http://dx.doi.org/10.7554/eLife.55325] [PMID: 32441252]
[39]
Haapaniemi E, Botla S, Persson J, Schmierer B, Taipale J. CRISPR-Cas9 genome editing induces a p53-mediated DNA damage response. Nat Med 2018; 24(7): 927-30.
[http://dx.doi.org/10.1038/s41591-018-0049-z] [PMID: 29892067]
[40]
Uusi-Mäkelä MIE, Barker HR, Bäuerlein CA, Häkkinen T, Nykter M, Rämet M. Chromatin accessibility is associated with CRISPR-Cas9 efficiency in the zebrafish (Danio rerio). PLoS One 2018; 13(4): e0196238.
[http://dx.doi.org/10.1371/journal.pone.0196238] [PMID: 29684067]
[41]
Wu X, Scott DA, Kriz AJ, et al. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat Biotechnol 2014; 32(7): 670-6.
[http://dx.doi.org/10.1038/nbt.2889] [PMID: 24752079]
[42]
Liu G, Yin K, Zhang Q, Gao C, Qiu J-L. Modulating chromatin accessibility by transactivation and targeting proximal dsgRNAs enhances Cas9 editing efficiency in vivo. Genome Biol 2019; 20(1): 145.
[http://dx.doi.org/10.1186/s13059-019-1762-8] [PMID: 31349852]
[43]
O’Geen H, Henry IM, Bhakta MS, Meckler JF, Segal DJ. A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture. Nucleic Acids Res 2015; 43(6): 3389-404.
[http://dx.doi.org/10.1093/nar/gkv137] [PMID: 25712100]
[44]
Kallimasioti-Pazi EM, Thelakkad Chathoth K, Taylor GC, et al. Heterochromatin delays CRISPR-Cas9 mutagenesis but does not influence the outcome of mutagenic DNA repair. PLoS Biol 2018; 16(12): e2005595.
[http://dx.doi.org/10.1371/journal.pbio.2005595] [PMID: 30540740]
[45]
Daer RM, Cutts JP, Brafman DA, Haynes KA. The impact of chromatin dynamics on cas9-mediated genome editing in human cells. ACS Synth Biol 2017; 6(3): 428-38.
[http://dx.doi.org/10.1021/acssynbio.5b00299] [PMID: 27783893]
[46]
Burman B, Zhang ZZ, Pegoraro G, Lieb JD, Misteli T. Histone modifications predispose genome regions to breakage and translocation. Genes Dev 2015; 29(13): 1393-402.
[http://dx.doi.org/10.1101/gad.262170.115] [PMID: 26104467]
[47]
Barkal AA, Srinivasan S, Hashimoto T, Gifford DK, Sherwood RI. Cas9 functionally opens chromatin. PLoS One 2016; 11(3): e0152683.
[http://dx.doi.org/10.1371/journal.pone.0152683] [PMID: 27031353]
[48]
Brinkman EK, Chen T, de Haas M, Holland HA, Akhtar W, van Steensel B. Kinetics and fidelity of the repair of cas9-induced double-strand dna breaks. Mol Cell 2018; 70(5): 801-13.e6.
[http://dx.doi.org/10.1016/j.molcel.2018.04.016] [PMID: 29804829]
[49]
Lanigan TM, Kopera HC, Saunders TL. Principles of genetic engineering. Genes (Basel) 2020; 11(3): 291.
[http://dx.doi.org/10.3390/genes11030291] [PMID: 32164255]
[50]
Gaudelli NM, Komor AC, Rees HA, et al. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature 2017; 551(7681): 464-71.
[http://dx.doi.org/10.1038/nature24644] [PMID: 29160308]
[51]
Zhang G, Zhou Z, Wei W. In vivo ways to unveil off-targets. Cell Res 2019; 29(5): 339-40.
[http://dx.doi.org/10.1038/s41422-019-0159-2] [PMID: 30890764]
[52]
Hendel A, Kildebeck EJ, Fine EJ, et al. Quantifying genome-editing outcomes at endogenous loci with SMRT sequencing. Cell Rep 2014; 7(1): 293-305.
[http://dx.doi.org/10.1016/j.celrep.2014.02.040] [PMID: 24685129]
[53]
Ardui S, Ameur A, Vermeesch JR, Hestand MS. Single molecule real-time (SMRT) sequencing comes of age: Applications and utilities for medical diagnostics. Nucleic Acids Res 2018; 46(5): 2159-68.
[http://dx.doi.org/10.1093/nar/gky066] [PMID: 29401301]
[54]
Cho SW, Kim S, Kim JM, Kim J-S. Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat Biotechnol 2013; 31(3): 230-2.
[http://dx.doi.org/10.1038/nbt.2507] [PMID: 23360966]
[55]
Vouillot L, Thélie A, Pollet N. Comparison of T7E1 and surveyor mismatch cleavage assays to detect mutations triggered by engineered nucleases. G3 (Bethesda) 2015; 5(3): 407-15.
[http://dx.doi.org/10.1534/g3.114.015834] [PMID: 25566793]
[56]
Miller JC, Tan S, Qiao G, et al. A TALE nuclease architecture for efficient genome editing. Nat Biotechnol 2011; 29(2): 143-8.
[http://dx.doi.org/10.1038/nbt.1755] [PMID: 21179091]
[57]
Duan J, Lu G, Xie Z, et al. Genome-wide identification of CRISPR/Cas9 off-targets in human genome. Cell Res 2014; 24(8): 1009-12.
[http://dx.doi.org/10.1038/cr.2014.87] [PMID: 24980957]
[58]
Tsai SQ, Zheng Z, Nguyen NT, et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol 2015; 33(2): 187-97.
[http://dx.doi.org/10.1038/nbt.3117] [PMID: 25513782]
[59]
Frock RL, Hu J, Meyers RM, Ho Y-JJ, Kii E, Alt FW. Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases. Nat Biotechnol 2015; 33(2): 179-86.
[http://dx.doi.org/10.1038/nbt.3101] [PMID: 25503383]
[60]
Schmidt M, Schwarzwaelder K, Bartholomae C, et al. High-resolution insertion-site analysis by linear amplification-mediated PCR (LAM-PCR). Nat Methods 2007; 4(12): 1051-7.
[http://dx.doi.org/10.1038/nmeth1103] [PMID: 18049469]
[61]
Osborn MJ, Starker CG, McElroy AN, et al. TALEN-based gene correction for epidermolysis bullosa. Mol Ther 2013; 21(6): 1151-9.
[http://dx.doi.org/10.1038/mt.2013.56] [PMID: 23546300]
[62]
Wang X, Wang Y, Wu X, et al. Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors. Nat Biotechnol 2015; 33(2): 175-8.
[http://dx.doi.org/10.1038/nbt.3127] [PMID: 25599175]
[63]
Kim D, Bae S, Park J, et al. Digenome-seq Genome-wide profiling of CRISPR-Cas9 off-target effects in human cells. Nat Methods 2015; 12(3): 237-243, 1, 243.
[http://dx.doi.org/10.1038/nmeth.3284] [PMID: 25664545]
[64]
Yan WX, Mirzazadeh R, Garnerone S, et al. BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks. Nat Commun 2017; 8: 15058.
[http://dx.doi.org/10.1038/ncomms15058] [PMID: 28497783]
[65]
Tsai SQ, Nguyen NT, Malagon-Lopez J, Topkar VV, Aryee MJ, Joung JK. CIRCLE-seq: A highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets. Nat Methods 2017; 14(6): 607-14.
[http://dx.doi.org/10.1038/nmeth.4278] [PMID: 28459458]
[66]
Wienert B, Wyman SK, Richardson CD, et al. Unbiased detection of CRISPR off-targets in vivo using discover-seq. Scince 2019; 364(2019): 286-9.
[67]
Zuo E, Sun Y, Wei W, et al. GOTI, a method to identify genome-wide off-target effects of genome editing in mouse embryos. Nat Protoc 2020; 15(9): 3009-29.
[http://dx.doi.org/10.1038/s41596-020-0361-1] [PMID: 32796939]
[68]
Xin H, Wan T, Ping Y. Off-Targeting of Base Editors: BE3 but not ABE induces substantial off-target single nucleotide variants. Signal Transduct Target Ther 2019; 4: 9.
[69]
Lin J, Wong K-C. Off-target predictions in CRISPR-Cas9 gene editing using deep learning. Bioinformatics 2018; 34(17): i656-63.
[http://dx.doi.org/10.1093/bioinformatics/bty554] [PMID: 30423072]
[70]
Listgarten J, Weinstein M, Kleinstiver BP, et al. Prediction of off-target activities for the end-to-end design of CRISPR guide RNAs. Nat Biomed Eng 2018; 2(1): 38-47.
[http://dx.doi.org/10.1038/s41551-017-0178-6] [PMID: 29998038]
[71]
Doench JG, Fusi N, Sullender M, et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol 2016; 34(2): 184-91.
[http://dx.doi.org/10.1038/nbt.3437] [PMID: 26780180]
[72]
Bae S, Park J, Kim J-S. Cas-OFFinder: A fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 2014; 30(10): 1473-5.
[http://dx.doi.org/10.1093/bioinformatics/btu048] [PMID: 24463181]
[73]
Montague TG, Cruz JM, Gagnon JA, Church GM, Valen E. CHOPCHOP: A CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res 2014; 42(Web Server issue): W401-7.
[http://dx.doi.org/10.1093/nar/gku410] [PMID: 24861617]
[74]
Labun K, Montague TG, Gagnon JA, Thyme SB, Valen E. CHOPCHOP v2: A web tool for the next generation of CRISPR genome engineering. Nucleic Acids Res 2016; 44(W1): W272-6.
[http://dx.doi.org/10.1093/nar/gkw398] [PMID: 27185894]
[75]
Labun K, Montague TG, Krause M, Torres Cleuren YN, Tjeldnes H, Valen E. CHOPCHOP v3: Expanding the CRISPR web toolbox beyond genome editing. Nucleic Acids Res 2019; 47(W1): W171-4.
[http://dx.doi.org/10.1093/nar/gkz365] [PMID: 31106371]
[76]
Liu H, Wei Z, Dominguez A, Li Y, Wang X, Qi LS. CRISPR-ERA: A comprehensive design tool for CRISPR-mediated gene editing, repression and activation. Bioinformatics 2015; 31(22): 3676-8.
[http://dx.doi.org/10.1093/bioinformatics/btv423] [PMID: 26209430]
[77]
Lei Y, Lu L, Liu H-Y, Li S, Xing F, Chen L-L. CRISPR-P: A web tool for synthetic single-guide RNA design of CRISPR-system in plants. Mol Plant 2014; 7(9): 1494-6.
[http://dx.doi.org/10.1093/mp/ssu044] [PMID: 24719468]
[78]
Heigwer F, Kerr G, Boutros M. E-CRISP: Fast CRISPR target site identification. Nat Methods 2014; 11(2): 122-3.
[http://dx.doi.org/10.1038/nmeth.2812] [PMID: 24481216]
[79]
Hsu PD, Scott DA, Weinstein JA, et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 2013; 31(9): 827-32.
[http://dx.doi.org/10.1038/nbt.2647] [PMID: 23873081]
[80]
Liu G, Zhang Y, Zhang T. Computational approaches for effective CRISPR guide RNA design and evaluation. Comput Struct Biotechnol J 2019; 18: 35-44.
[http://dx.doi.org/10.1016/j.csbj.2019.11.006] [PMID: 31890142]
[81]
Haeussler M, Schönig K, Eckert H, et al. Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol 2016; 17(1): 148.
[http://dx.doi.org/10.1186/s13059-016-1012-2] [PMID: 27380939]
[82]
Alkan F, Wenzel A, Anthon C, Havgaard JH, Gorodkin J. CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters. Genome Biol 2018; 19(1): 177.
[http://dx.doi.org/10.1186/s13059-018-1534-x] [PMID: 30367669]
[83]
Zhang D, Hurst T, Duan D, Chen S-J. Unified energetics analysis unravels SpCas9 cleavage activity for optimal gRNA design. Proc Natl Acad Sci USA 2019; 116(18): 8693-8.
[http://dx.doi.org/10.1073/pnas.1820523116] [PMID: 30988204]
[84]
Abadi S, Yan WX, Amar D, Mayrose I. A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action. PLOS Comput Biol 2017; 13(10): e1005807.
[http://dx.doi.org/10.1371/journal.pcbi.1005807] [PMID: 29036168]
[85]
Chuai G, Ma H, Yan J, et al. DeepCRISPR: Optimized CRISPR guide RNA design by deep learning. Genome Biol 2018; 19(1): 80.
[http://dx.doi.org/10.1186/s13059-018-1459-4] [PMID: 29945655]
[86]
Smith RH, Chen Y-C, Seifuddin F, et al. Genome-wide analysis of off-target crispr/cas9 activity in single-cell-derived human hematopoietic stem and progenitor cell clones. Genes (Basel) 2020; 11(12): E1501.
[http://dx.doi.org/10.3390/genes11121501] [PMID: 33322084]
[87]
Cromwell CR, Sung K, Park J, et al. Incorporation of bridged nucleic acids into CRISPR RNAs improves Cas9 endonuclease specificity. Nat Commun 2018; 9(1): 1448.
[http://dx.doi.org/10.1038/s41467-018-03927-0] [PMID: 29654299]
[88]
Ghorbal M, Gorman M, Macpherson CR, Martins RM, Scherf A, Lopez-Rubio J-J. Genome editing in the human malaria parasite plasmodium falciparum using the CRISPR-Cas9 system. Nat Biotechnol 2014; 32(8): 819-21.
[http://dx.doi.org/10.1038/nbt.2925] [PMID: 24880488]
[89]
Jiang F, Zhou K, Ma L, Gressel S, Doudna JA. A cas9{\textendash}guide RNA complex preorganized for target dna recognition. Science 2015; 348(6242): 1477-81.
[90]
Sternberg SH, LaFrance B, Kaplan M, Doudna JA. Conformational control of DNA target cleavage by CRISPR-Cas9. Nature 2015; 527(7576): 110-3.
[http://dx.doi.org/10.1038/nature15544] [PMID: 26524520]
[91]
Wang T, Wei JJ, Sabatini DM, Lander ES. Genetic screens in human cells using the CRISPR-Cas9 system. Science 2014; 343(6166): 80-4.
[http://dx.doi.org/10.1126/science.1246981] [PMID: 24336569]
[92]
Ran FA, Cong L, Yan WX, et al. In vivo genome editing using Staphylococcus aureus Cas9. Nature 2015; 520(7546): 186-91.
[http://dx.doi.org/10.1038/nature14299] [PMID: 25830891]
[93]
Moreno-Mateos MA, Vejnar CE, Beaudoin J-D, et al. CRISPRscan: Designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat Methods 2015; 12(10): 982-8.
[http://dx.doi.org/10.1038/nmeth.3543] [PMID: 26322839]
[94]
Guilinger JP, Thompson DB, Liu DR. Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nat Biotechnol 2014; 32(6): 577-82.
[http://dx.doi.org/10.1038/nbt.2909] [PMID: 24770324]
[95]
Tsai SQ, Wyvekens N, Khayter C, et al. Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Nat Biotechnol 2014; 32(6): 569-76.
[http://dx.doi.org/10.1038/nbt.2908] [PMID: 24770325]
[96]
Lone BA, Karna SKL, Ahmad F, Shahi N, Pokharel YR. CRISPR/Cas9 system: A bacterial tailor for genomic engineering. Genet Res Int 2018; 2018: 3797214.
[97]
Wang H, La Russa M, Qi LS. CRISPR/Cas9 in genome editing and beyond. Annu Rev Biochem 2016; 85: 227-64.
[http://dx.doi.org/10.1146/annurev-biochem-060815-014607] [PMID: 27145843]
[98]
Ortinski PI, O’Donovan B, Dong X, Kantor B. Integrase-deficient lentiviral vector as an all-in-one platform for highly efficient crispr/cas9-mediated gene editing. Mol Ther Methods Clin Dev 2017; 5: 153-64.
[http://dx.doi.org/10.1016/j.omtm.2017.04.002] [PMID: 28497073]
[99]
Cao J, Wu L, Zhang S-M, et al. An easy and efficient inducible CRISPR/Cas9 platform with improved specificity for multiple gene targeting. Nucleic Acids Res 2016; 44(19): e149-9.
[http://dx.doi.org/10.1093/nar/gkw660] [PMID: 27458201]
[100]
Davis KM, Pattanayak V, Thompson DB, Zuris JA, Liu DR. Small molecule-triggered Cas9 protein with improved genome-editing specificity. Nat Chem Biol 2015; 11(5): 316-8.
[http://dx.doi.org/10.1038/nchembio.1793] [PMID: 25848930]
[101]
Senturk S, Shirole NH, Nowak DG, et al. Rapid and tunable method to temporally control gene editing based on conditional Cas9 stabilization. Nat Commun 2017; 8: 14370.
[http://dx.doi.org/10.1038/ncomms14370] [PMID: 28224990]
[102]
Shin J, Jiang F, Liu J-J, et al. Disabling Cas9 by an anti-CRISPR DNA mimic. Sci Adv 2017; 3(7): e1701620.
[http://dx.doi.org/10.1126/sciadv.1701620] [PMID: 28706995]
[103]
Abudayyeh OO, Gootenberg JS, Konermann S, et al. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science 2016; 353(6299): aaf5573-3.
[http://dx.doi.org/10.1126/science.aaf5573] [PMID: 27256883]
[104]
Slaymaker IM, Gao L, Zetsche B, Scott DA, Yan WX, Zhang F. Rationally engineered Cas9 nucleases with improved specificity. Science 2016; 351(2016): 84 LP-.
[105]
Wang L, Xue W, Yan L, et al. Enhanced base editing by co-expression of free uracil DNA glycosylase inhibitor. Cell Res 2017; 27(10): 1289-92.
[http://dx.doi.org/10.1038/cr.2017.111] [PMID: 28849781]
[106]
Grünewald J, Zhou R, Iyer S, et al. CRISPR DNA base editors with reduced RNA off-target and self-editing activities. Nat Biotechnol 2019; 37(9): 1041-8.
[http://dx.doi.org/10.1038/s41587-019-0236-6] [PMID: 31477922]
[107]
Cho SW, Kim S, Kim Y, et al. Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res 2014; 24(1): 132-41.
[http://dx.doi.org/10.1101/gr.162339.113] [PMID: 24253446]
[108]
Zetsche B, Gootenberg JS, Abudayyeh OO, et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 2015; 163(3): 759-71.
[http://dx.doi.org/10.1016/j.cell.2015.09.038] [PMID: 26422227]
[109]
Maruyama T, Dougan SK, Truttmann MC, Bilate AM, Ingram JR, Ploegh HL. Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining. Nat Biotechnol 2015; 33(5): 538-42.
[http://dx.doi.org/10.1038/nbt.3190] [PMID: 25798939]
[110]
Yu C, Liu Y, Ma T, et al. Small molecules enhance CRISPR genome editing in pluripotent stem cells. Cell Stem Cell 2015; 16(2): 142-7.
[http://dx.doi.org/10.1016/j.stem.2015.01.003] [PMID: 25658371]
[111]
Hendel A, Bak RO, Clark JT, et al. Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells. Nat Biotechnol 2015; 33(9): 985-9.
[http://dx.doi.org/10.1038/nbt.3290] [PMID: 26121415]
[112]
Pineda M, Lear A, Collins JP, Kiani S. Safe CRISPR: Challenges and possible solutions. Trends Biotechnol 2019; 37(4): 389-401.
[http://dx.doi.org/10.1016/j.tibtech.2018.09.010] [PMID: 30352704]
[113]
Scott DA, Zhang F. Implications of human genetic variation in CRISPR-based therapeutic genome editing. Nat Med 2017; 23(9): 1095-101.
[http://dx.doi.org/10.1038/nm.4377] [PMID: 28759051]
[114]
Iyer V, Boroviak K, Thomas M, et al. No unexpected CRISPR-Cas9 off-target activity revealed by trio sequencing of gene-edited mice. PLoS Genet 2018; 14(7): e1007503.
[http://dx.doi.org/10.1371/journal.pgen.1007503] [PMID: 29985941]
[115]
Kosicki M, Tomberg K, Bradley A. Repair of double-strand breaks induced by CRISPR-Cas9 leads to large deletions and complex rearrangements. Nat Biotechnol 2018; 36(8): 765-71.
[http://dx.doi.org/10.1038/nbt.4192] [PMID: 30010673]
[116]
Hahn F, Nekrasov V. CRISPR/Cas precision: Do we need to worry about off-targeting in plants? Plant Cell Rep 2019; 38(4): 437-41.
[http://dx.doi.org/10.1007/s00299-018-2355-9] [PMID: 30426198]
[117]
Liang P, Sun H, Sun Y, et al. Effective gene editing by high-fidelity base editor 2 in mouse zygotes. Protein Cell 2017; 8(8): 601-11.
[http://dx.doi.org/10.1007/s13238-017-0418-2] [PMID: 28585179]
[118]
Zhang Q, Xing H-L, Wang Z-P, et al. Potential high-frequency off-target mutagenesis induced by CRISPR/Cas9 in arabidopsis and its prevention. Plant Mol Biol 2018; 96(4-5): 445-56.
[http://dx.doi.org/10.1007/s11103-018-0709-x] [PMID: 29476306]
[119]
Nekrasov V, Wang C, Win J, Lanz C, Weigel D, Kamoun S. Rapid generation of a transgene-free powdery mildew resistant tomato by genome deletion. Sci Rep 2017; 7(1): 482.
[http://dx.doi.org/10.1038/s41598-017-00578-x] [PMID: 28352080]
[120]
Young J, Zastrow-Hayes G, Deschamps S, et al. CRISPR-Cas9 editing in maize: Systematic evaluation of off-target activity and its relevance in crop improvement. Sci Rep 2019; 9(1): 6729.
[http://dx.doi.org/10.1038/s41598-019-43141-6] [PMID: 31040331]
[121]
Horlbeck MA, Witkowsky LB, Guglielmi B, et al. Nucleosomes impede Cas9 access to DNA in vivo and in vitro. eLife 2016; 5: e12677.
[http://dx.doi.org/10.7554/eLife.12677] [PMID: 26987018]
[122]
Yarrington RM, Verma S, Schwartz S, Trautman JK, Carroll D. Nucleosomes inhibit target cleavage by CRISPR-Cas9 in vivo. Proc Natl Acad Sci USA 2018; 115(38): 9351-8.
[http://dx.doi.org/10.1073/pnas.1810062115] [PMID: 30201707]
[123]
Cong L, Ran FA, Cox D, et al. Multiplex genome engineering using crispr/cas systems. Science 2013; 339(2013): 819-23.
[124]
Cancellieri S, Canver MC, Bombieri N, Giugno R, Pinello L. CRISPRitz: Rapid, high-throughput and variant-aware in silico off-target site identification for CRISPR genome editing. Bioinformatics 2020; 36(7): 2001-8.
[http://dx.doi.org/10.1093/bioinformatics/btz867] [PMID: 31764961]
[125]
Singh R, Kuscu C, Quinlan A, Qi Y, Adli M. Cas9-chromatin binding information enables more accurate CRISPR off-target prediction. Nucleic Acids Res 2015; 43(18): e118-8.
[http://dx.doi.org/10.1093/nar/gkv575] [PMID: 26032770]
[126]
Stemmer M, Thumberger T, Del Sol Keyer M, Wittbrodt J, Mateo JL. CCTop: An intuitive, flexible and reliable CRISPR/Cas9 target prediction tool. PLoS One 2015; 10(4): e0124633.
[http://dx.doi.org/10.1371/journal.pone.0124633] [PMID: 25909470]
[127]
Gehrke JM, Cervantes O, Clement MK, et al. An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities. Nat Biotechnol 2018; 36(10): 977-82.
[http://dx.doi.org/10.1038/nbt.4199] [PMID: 30059493]
[128]
Komor AC, Zhao KT, Packer MS, et al. Improved base excision repair inhibition and bacteriophage Mu Gam protein yields C:G-to-T:A base editors with higher efficiency and product purity. Sci Adv 2017; 3(8): eaao4774.
[http://dx.doi.org/10.1126/sciadv.aao4774] [PMID: 28875174]
[129]
Rees HA, Komor AC, Yeh W-H, et al. Improving the DNA specificity and applicability of base editing through protein engineering and protein delivery. Nat Commun 2017; 8: 15790.
[http://dx.doi.org/10.1038/ncomms15790] [PMID: 28585549]

Rights & Permissions Print Cite
Article Metrics
53
1
© 2024 Bentham Science Publishers | Privacy Policy