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

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Review Article

A Review: Computational Approaches to Design sgRNA of CRISPR-Cas9

Author(s): Mohsin Ali Nasir, Samia Nawaz and Jian Huang*

Volume 17, Issue 1, 2022

Published on: 31 May, 2021

Page: [2 - 18] Pages: 17

DOI: 10.2174/1574893616666210601105553

Price: $65

Abstract

Clustered regularly interspaced short palindromic repeats along with CRISPR-associated protein mechanisms preserve the memory of previous experiences with DNA invaders, in particular spacers that are embedded in CRISPR arrays between coordinate repeats. There has been a fast progression in the comprehension of this immune system and its implementations; however, there are numerous points of view that anticipate explanations to make the field an energetic research zone. The efficiency of CRISPR-Cas depends upon well-considered single guide RNA; for this purpose, many bioinformatics methods and tools are created to support the design of greatly active and precise single guide RNA. Insilico single guide RNA architecture is a crucial point for effective gene editing by means of the CRISPR technique. Persistent attempts have been made to improve in-silico single guide RNA formulation having great on-target effectiveness and decreased off-target effects. This review offers a summary of the CRISPR computational tools to help different researchers pick a specific tool for their work according to pros and cons, along with new thoughts to make new computational tools to overcome all existing limitations.

Keywords: CRISPR-Cas9, sgRNA, computational tools, off-target effects, on-target, protein.

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[1]
Deveau H, Garneau JE, Moineau S. CRISPR/Cas system and its role in phage-bacteria interactions. Annu Rev Microbiol 2010; 64: 475-93.
[http://dx.doi.org/10.1146/annurev.micro.112408.134123] [PMID: 20528693]
[2]
Marraffini LA, Sontheimer EJ. CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat Rev Genet 2010; 11(3): 181-90.
[http://dx.doi.org/10.1038/nrg2749] [PMID: 20125085]
[3]
Makarova KS, Wolf YI, Koonin EV. The basic building blocks and evolution of CRISPR–Cas systems. Biochem Soc Trans 2013; 41(6): 1392-400.
[http://dx.doi.org/10.1042/BST20130038]
[4]
Barrangou R, Marraffini LA. CRISPR-Cas systems: Prokaryotes upgrade to adaptive immunity. Mol Cell 2014; 54(2): 234-44.
[http://dx.doi.org/10.1016/j.molcel.2014.03.011] [PMID: 24766887]
[5]
Anantharaman V, Makarova KS, Burroughs AM, Koonin EV, Aravind L. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Biol Direct 2013; 8(1): 15.
[http://dx.doi.org/10.1186/1745-6150-8-15] [PMID: 23768067]
[6]
Jiang F, Doudna JA. CRISPR–Cas9 structures and mechanisms. Annu Rev Biophys 2017; 46: 505-29.
[http://dx.doi.org/10.1146/annurev-biophys-062215-010822] [PMID: 28375731]
[7]
Mir A, Edraki A, Lee J, Sontheimer EJ. Type II-C CRISPR-Cas9 Biology, mechanism, and application. ACS Chem Biol 2018; 13(2): 357-65.
[http://dx.doi.org/10.1021/acschembio.7b00855] [PMID: 29202216]
[8]
Chyou T, Brown CM. Prediction and diversity of tracrRNAs from type II CRISPR-Cas systems. RNA Biol 2018; 16(4): 423-34.
[9]
Barrangou R, Fremaux C, Deveau H, et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 2007; 315(5819): 1709-12.
[http://dx.doi.org/10.1126/science.1138140] [PMID: 17379808]
[10]
Hale CR, Zhao P, Olson S, et al. RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell 2009; 139(5): 945-56.
[http://dx.doi.org/10.1016/j.cell.2009.07.040] [PMID: 19945378]
[11]
Bolotin A, Quinquis B, Sorokin A, Ehrlich SD. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology (Reading) 2005; 151(Pt 8): 2551-61.
[http://dx.doi.org/10.1099/mic.0.28048-0] [PMID: 16079334]
[12]
Brouns SJ, Jore MM, Lundgren M, et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 2008; 321(5891): 960-4.
[http://dx.doi.org/10.1126/science.1159689] [PMID: 18703739]
[13]
Rath D, Amlinger L, Rath A, Lundgren M. The CRISPR-Cas immune system: biology, mechanisms and applications. Biochimie 2015; 117: 119-28.
[http://dx.doi.org/10.1016/j.biochi.2015.03.025] [PMID: 25868999]
[14]
Delneri D, Tomlin GC, Wixon JL, et al. Exploring redundancy in the yeast genome: an improved strategy for use of the cre-loxP system. Gene 2000; 252(1-2): 127-35.
[http://dx.doi.org/10.1016/S0378-1119(00)00217-1 PMID: 10903444]
[15]
Carte J, Wang R, Li H, Terns RM, Terns MP. Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. Genes Dev 2008; 22(24): 3489-96.
[http://dx.doi.org/10.1101/gad.1742908] [PMID: 19141480]
[16]
Haurwitz RE, Jinek M, Wiedenheft B, Zhou K, Doudna JA. Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science 2010; 329(5997): 1355-8.
[http://dx.doi.org/10.1126/science.1192272] [PMID: 20829488]
[17]
Gesner EM, Schellenberg MJ, Garside EL, George MM, Macmillan AM. Recognition and maturation of effector RNAs in a CRISPR interference pathway. Nat Struct Mol Biol 2011; 18(6): 688-92.
[http://dx.doi.org/10.1038/nsmb.2042] [PMID: 21572444]
[18]
Sashital DG, Jinek M, Doudna JA. An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3. Nat Struct Mol Biol 2011; 18(6): 680-7.
[http://dx.doi.org/10.1038/nsmb.2043] [PMID: 21572442]
[19]
Wang R, Preamplume G, Terns MP, Terns RM, Li H. Interaction of the Cas6 riboendonuclease with CRISPR RNAs: recognition and cleavage. Structure 2011; 19(2): 257-64.
[http://dx.doi.org/10.1016/j.str.2010.11.014] [PMID: 21300293]
[20]
Hale C, Kleppe K, Terns RM, Terns MP. Prokaryotic silencing (psi)RNAs in Pyrococcus furiosus. RNA 2008; 14(12): 2572-9.
[http://dx.doi.org/10.1261/rna.1246808] [PMID: 18971321]
[21]
Jore MM, Lundgren M, van Duijn E, et al. Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat Struct Mol Biol 2011; 18(5): 529-36.
[http://dx.doi.org/10.1038/nsmb.2019] [PMID: 21460843]
[22]
Lintner NG, Kerou M, Brumfield SK, et al. Structural and functional characterization of an archaeal clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for antiviral defense (CASCADE). J Biol Chem 2011; 286(24): 21643-56.
[http://dx.doi.org/10.1074/jbc.M111.238485] [PMID: 21507944]
[23]
Wiedenheft B, van Duijn E, Bultema JB, et al. RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions. Proc Natl Acad Sci USA 2011; 108(25): 10092-7.
[http://dx.doi.org/10.1073/pnas.1102716108] [PMID: 21536913]
[24]
Wiedenheft B, Lander GC, Zhou K, et al. Structures of the RNA-guided surveillance complex from a bacterial immune system. Nature 2011; 477(7365): 486-9.
[http://dx.doi.org/10.1038/nature10402] [PMID: 21938068]
[25]
Yang L, Yang JL, Byrne S, et al. CRISPR/Cas9‐directed genome editing of cultured cells. Curr Protoc Mol Biol 2014; 107(1): 31.1.1-17.
[http://dx.doi.org/10.1002/0471142727.mb3101s107]
[26]
Heler R, Samai P, Modell JW, et al. Cas9 specifies functional viral targets during CRISPR-Cas adaptation. Nature 2015; 519(7542): 199-202.
[http://dx.doi.org/10.1038/nature14245] [PMID: 25707807]
[27]
Amitai G, Sorek R. CRISPR-Cas adaptation: insights into the mechanism of action. Nat Rev Microbiol 2016; 14(2): 67-76.
[http://dx.doi.org/10.1038/nrmicro.2015.14] [PMID: 26751509]
[28]
Vickers NJ. Animal communication: when i’m calling you, will you answer too? Curr Biol 2017; 27(14): R713-5.
[http://dx.doi.org/10.1016/j.cub.2017.05.064] [PMID: 28743020]
[29]
Charpentier E, Richter H, van der Oost J, White MF. Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity. FEMS Microbiol Rev 2015; 39(3): 428-41.
[http://dx.doi.org/10.1093/femsre/fuv023] [PMID: 25994611]
[30]
Fonfara I, Richter H, Bratovič M, Le Rhun A, Charpentier E. The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA. Nature 2016; 532(7600): 517-21.
[http://dx.doi.org/10.1038/nature17945] [PMID: 27096362]
[31]
East-Seletsky A, O’Connell MR, Knight SC, et al. Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature 2016; 538(7624): 270-3.
[http://dx.doi.org/10.1038/nature19802] [PMID: 27669025]
[32]
Swarts DC, van der Oost J, Jinek M. Structural basis for guide RNA processing and seed-dependent DNA targeting by CRISPRCas12a. Mol Cell 2017; 66(2): 221-33.e4
[33]
Makarova KS, Haft DH, Barrangou R, et al. Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol 2011; 9(6): 467-77.
[http://dx.doi.org/10.1038/nrmicro2577] [PMID: 21552286]
[34]
Barrangou R. CRISPR-Cas systems and RNA-guided interference. Wiley Interdiscip Rev RNA 2013; 4(3): 267-78.
[http://dx.doi.org/10.1002/wrna.1159] [PMID: 23520078]
[35]
Plagens A, Richter H, Charpentier E, Randau L. DNA and RNA interference mechanisms by CRISPR-Cas surveillance complexes. FEMS Microbiol Rev 2015; 39(3): 442-63.
[http://dx.doi.org/10.1093/femsre/fuv019] [PMID: 25934119]
[36]
Nishimasu H, Nureki O. Structures and mechanisms of CRISPR RNA-guided effector nucleases. Curr Opin Struct Biol 2017; 43: 68-78.
[http://dx.doi.org/10.1016/j.sbi.2016.11.013] [PMID: 27912110]
[37]
Han W, Li Y, Deng L, et al. A type III-B CRISPR-Cas effector complex mediating massive target DNA destruction. Nucleic Acids Res 2017; 45(4): 1983-93.
[PMID: 27986854]
[38]
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
[http://dx.doi.org/10.1126/science.aaf5573] [PMID: 27256883]
[39]
Smargon AA, Cox DBT, Pyzocha NK, et al. Cas13b is a type VI-B CRISPR-associated RNA-guided RNase differentially regulated by accessory proteins Csx27 and Csx28. Molecular cell 2017; 65(4): 618-30.e7
[40]
Westra ER, Swarts DC, Staals RH, Jore MM, Brouns SJ, van der Oost J. The CRISPRs, they are a-changin’: how prokaryotes generate adaptive immunity. Annu Rev Genet 2012; 46: 311-39.
[http://dx.doi.org/10.1146/annurev-genet-110711-155447] [PMID: 23145983]
[41]
Wiedenheft B, Sternberg SH, Doudna JA. RNA-guided genetic silencing systems in bacteria and archaea. Nature 2012; 482(7385): 331-8.
[http://dx.doi.org/10.1038/nature10886] [PMID: 22337052]
[42]
Garneau JE, Dupuis MÈ, Villion M, et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 2010; 468(7320): 67-71.
[http://dx.doi.org/10.1038/nature09523] [PMID: 21048762]
[43]
Magadán AH, Dupuis MÈ, Villion M, Moineau S. Cleavage of phage DNA by the Streptococcus thermophilus CRISPR3-Cas system. PLoS One 2012; 7(7)e40913
[http://dx.doi.org/10.1371/journal.pone.0040913] [PMID: 22911717]
[44]
Bhaya D, Davison M, Barrangou R. CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annu Rev Genet 2011; 45: 273-97.
[http://dx.doi.org/10.1146/annurev-genet-110410-132430] [PMID: 22060043]
[45]
Terns MP, Terns RM. CRISPR-based adaptive immune systems. Curr Opin Microbiol 2011; 14(3): 321-7.
[http://dx.doi.org/10.1016/j.mib.2011.03.005] [PMID: 21531607]
[46]
Gasiunas G, Barrangou R, Horvath P, Siksnys V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci USA 2012; 109(39): E2579-86.
[http://dx.doi.org/10.1073/pnas.1208507109] [PMID: 22949671]
[47]
Jinek M, Chylinski K, Fonfara I, et al. A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science 2012; 337(6096): 816-21.
[http://dx.doi.org/10.1126/science.1225829]
[48]
Mojica FJM, Díez-Villaseñor C, García-Martínez J, Almendros C. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 2009; 155(Pt 3): 733-40.
[http://dx.doi.org/10.1099/mic.0.023960-0] [PMID: 19246744]
[49]
Yin S, Jensen MA, Bai J, Debroy C, Barrangou R, Dudley EG. The evolutionary divergence of Shiga toxin-producing Escherichia coli is reflected in clustered regularly interspaced short palindromic repeat (CRISPR) spacer composition. Appl Environ Microbiol 2013; 79(18): 5710-20.
[http://dx.doi.org/10.1128/AEM.00950-13] [PMID: 23851088]
[50]
Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 2014; 507(7490): 62-7.
[http://dx.doi.org/10.1038/nature13011] [PMID: 24476820]
[51]
Zhang J, Rouillon C, Kerou M, et al. Structure and mechanism of the CMR complex for CRISPR-mediated antiviral immunity. Mol Cell 2012; 45(3): 303-13.
[http://dx.doi.org/10.1016/j.molcel.2011.12.013] [PMID: 22227115]
[52]
Staals RHJ, Agari Y, Maki-Yonekura S, et al. Structure and activity of the RNA-targeting Type III-B CRISPR-Cas complex of Thermus thermophilus. Mol Cell 2013; 52(1): 135-45.
[http://dx.doi.org/10.1016/j.molcel.2013.09.013] [PMID: 24119403]
[53]
Spilman M, Cocozaki A, Hale C, et al. Structure of an RNA silencing complex of the CRISPR-Cas immune system. Mol Cell 2013; 52(1): 146-52.
[http://dx.doi.org/10.1016/j.molcel.2013.09.008] [PMID: 24119404]
[54]
Koonin EV, Makarova KS, Zhang F. Diversity, classification and evolution of CRISPR-Cas systems. Curr Opin Microbiol 2017; 37: 67-78.
[http://dx.doi.org/10.1016/j.mib.2017.05.008] [PMID: 28605718]
[55]
Makarova KS, Wolf YI, Alkhnbashi OS, et al. An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol 2015; 13(11): 722-36.
[http://dx.doi.org/10.1038/nrmicro3569] [PMID: 26411297]
[56]
Makarova KS, Koonin EV. Annotation and classification of CRISPR-Cas systemsCRISPR. Springer 2015; pp. 47-75.
[http://dx.doi.org/10.1007/978-1-4939-2687-9_4]
[57]
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.
[58]
Dong Z-Q, Chen TT, Zhang J, et al. Establishment of a highly efficient virus-inducible CRISPR/Cas9 system in insect cells. Antiviral Res 2016; 130: 50-7.
[http://dx.doi.org/10.1016/j.antiviral.2016.03.009] [PMID: 26979473]
[59]
Port F, Bullock SL. Augmenting CRISPR applications in Drosophila with tRNA-flanked sgRNAs. Nat Methods 2016; 13(10): 852-4.
[http://dx.doi.org/10.1038/nmeth.3972] [PMID: 27595403]
[60]
Ma S, Liu Y, Liu Y, et al. An integrated CRISPR Bombyx mori genome editing system with improved efficiency and expanded target sites. Insect Biochem Mol Biol 2017; 83: 13-20.
[http://dx.doi.org/10.1016/j.ibmb.2017.02.003] [PMID: 28189747]
[61]
Yamano T, Nishimasu H, Zetsche B, et al. Crystal structure of Cpf1 in complex with guide RNA and target DNA. Cell 2016; 165(4): 949-62.
[http://dx.doi.org/10.1016/j.cell.2016.04.003] [PMID: 27114038]
[62]
Deltcheva E, Chylinski K, Sharma CM, et al. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 2011; 471(7340): 602-7.
[http://dx.doi.org/10.1038/nature09886] [PMID: 21455174]
[63]
Gardner MJ, Shallom SJ, Carlton JM, et al. Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14. Nature 2002; 419(6906): 531-4.
[http://dx.doi.org/10.1038/nature01094] [PMID: 12368868]
[64]
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]
[65]
Shmakov S, Abudayyeh OO, Makarova KS, et al. Discovery and functional characterization of diverse class 2 CRISPR-Cas systems. Mol Cell 2015; 60(3): 385-97.
[http://dx.doi.org/10.1016/j.molcel.2015.10.008] [PMID: 26593719]
[66]
Biswas A, Fineran PC, Brown CM. Accurate computational prediction of the transcribed strand of CRISPR non-coding RNAs. Bioinformatics 2014; 30(13): 1805-13.
[http://dx.doi.org/10.1093/bioinformatics/btu114] [PMID: 24578404]
[67]
Anders C, Niewoehner O, Duerst A, Jinek M. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature 2014; 513(7519): 569-73.
[http://dx.doi.org/10.1038/nature13579] [PMID: 25079318]
[68]
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]
[69]
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]
[70]
Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 2012; 337(6096): 816-21.
[http://dx.doi.org/10.1126/science.1225829] [PMID: 22745249]
[71]
Yin K, Gao C, Qiu J-L. Progress and prospects in plant genome editing. Nat Plants 2017; 3(8): 17107.
[http://dx.doi.org/10.1038/nplants.2017.107] [PMID: 28758991]
[72]
Gao C. The future of CRISPR technologies in agriculture. Nat Rev Mol Cell Biol 2018; 19(5): 275-6.
[http://dx.doi.org/10.1038/nrm.2018.2] [PMID: 29382940]
[73]
Doudna JA, Charpentier E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 2014; 346(6213)1258096
[http://dx.doi.org/10.1126/science.1258096] [PMID: 25430774]
[74]
Eid A, Mahfouz MM. Genome editing: the road of CRISPR/Cas9 from bench to clinic. Exp Mol Med 2016; 48(10)e265
[http://dx.doi.org/10.1038/emm.2016.111] [PMID: 27741224]
[75]
Zhang J-P, Li XL, Li GH, et al. Efficient precise knockin with a double cut HDR donor after CRISPR/Cas9-mediated double-stranded DNA cleavage. Genome Biol 2017; 18(1): 35.
[http://dx.doi.org/10.1186/s13059-017-1164-8] [PMID: 28219395]
[76]
Pál C, Papp B, Lercher MJ. An integrated view of protein evolution. Nat Rev Genet 2006; 7(5): 337-48.
[http://dx.doi.org/10.1038/nrg1838] [PMID: 16619049]
[77]
Ma Y, Zhang J, Yin W, Zhang Z, Song Y, Chang X. Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells. Nat Methods 2016; 13(12): 1029-35.
[http://dx.doi.org/10.1038/nmeth.4027] [PMID: 27723754]
[78]
Hess GT, Tycko J, Yao D, Bassik MC. Methods and applications of CRISPR-mediated base editing in eukaryotic genomes. Mol Cell 2017; 68(1): 26-43.
[http://dx.doi.org/10.1016/j.molcel.2017.09.029] [PMID: 28985508]
[79]
Eid A, Alshareef S, Mahfouz MM. CRISPR base editors: Genome editing without double-stranded breaks. In: Biochem J. 2018; 475: pp. (11)1955-64.
[80]
O’Connell MR, Oakes BL, Sternberg SH, East-Seletsky A, Kaplan M, Doudna JA. Programmable RNA recognition and cleavage by CRISPR/Cas9. Nature 2014; 516(7530): 263-6.
[http://dx.doi.org/10.1038/nature13769] [PMID: 25274302]
[81]
Hu JH, Miller SM, Geurts MH, et al. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature 2018; 556(7699): 57-63.
[http://dx.doi.org/10.1038/nature26155] [PMID: 29512652]
[82]
Kleinstiver BP, Prew MS, Tsai SQ, et al. Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature 2015; 523(7561): 481-5.
[http://dx.doi.org/10.1038/nature14592] [PMID: 26098369]
[83]
Casalino L, Nierzwicki Ł, Jinek M, Palermo G. Catalytic mechanism of non-target DNA cleavage in CRISPR-Cas9 revealed by Ab Initio molecular dynamics. ACS Catal 2020; 10(22): 13596-605.
[http://dx.doi.org/10.1021/acscatal.0c03566] [PMID: 33520346]
[84]
Jinek M, Jiang F, Taylor DW, et al. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 2014; 343(6176)1247997
[http://dx.doi.org/10.1126/science.1247997] [PMID: 24505130]
[85]
Steitz TA, Steitz JA. A general two-metal-ion mechanism for catalytic RNA. Proc Natl Acad Sci USA 1993; 90(14): 6498-502.
[http://dx.doi.org/10.1073/pnas.90.14.6498] [PMID: 8341661]
[86]
Jiang F, Taylor DW, Chen JS, et al. Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage. Science 2016; 351(6275): 867-71.
[http://dx.doi.org/10.1126/science.aad8282] [PMID: 26841432]
[87]
Yang W. Nucleases: diversity of structure, function and mechanism. Q Rev Biophys 2011; 44(1): 1-93.
[http://dx.doi.org/10.1017/S0033583510000181] [PMID: 20854710]
[88]
Pérez A, Lankas F, Luque FJ, Orozco M. Towards a molecular dynamics consensus view of B-DNA flexibility. Nucleic Acids Res 2008; 36(7): 2379-94.
[http://dx.doi.org/10.1093/nar/gkn082] [PMID: 18299282]
[89]
Pérez A, Luque FJ, Orozco M. Dynamics of B-DNA on the microsecond time scale. J Am Chem Soc 2007; 129(47): 14739-45.
[http://dx.doi.org/10.1021/ja0753546] [PMID: 17985896]
[90]
Mura C, McCammon JA. Molecular dynamics of a kappaB DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation. Nucleic Acids Res 2008; 36(15): 4941-55.
[http://dx.doi.org/10.1093/nar/gkn473] [PMID: 18653524]
[91]
Ma Z, Palermo G, Adhireksan Z, et al. An organometallic compound which exhibits a DNA topology-dependent one-stranded intercalation mode. Angew Chem Int Ed Engl 2016; 55(26): 7441-4.
[http://dx.doi.org/10.1002/anie.201602145] [PMID: 27184539]
[92]
Palermo G, Miao Y, Walker RC, Jinek M, McCammon JA. CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations. Proc Natl Acad Sci USA 2017; 114(28): 7260-5.
[http://dx.doi.org/10.1073/pnas.1707645114] [PMID: 28652374]
[93]
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]
[94]
Mitchell BP, Hsu RV, Medrano MA, Zewde NT, Narkhede YB, Palermo G. Spontaneous embedding of DNA mismatches within the RNA: DNA hybrid of CRISPR-Cas9. Front Mol Biosci 2020; 7: 39.
[http://dx.doi.org/10.3389/fmolb.2020.00039] [PMID: 32258048]
[95]
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]
[96]
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]
[97]
Lin Y, Cradick TJ, Brown MT, et al. CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences. Nucleic Acids Res 2014; 42(11): 7473-85.
[http://dx.doi.org/10.1093/nar/gku402] [PMID: 24838573]
[98]
Manghwar H, Li B, Ding X, et al. CRISPR/Cas Systems in Genome Editing: Methodologies and tools for sgRNA design, off‐target evaluation, and strategies to mitigate off‐target effects. Adv Sci (Weinh) 2020; 7(6)1902312
[http://dx.doi.org/10.1002/advs.201902312] [PMID: 32195078]
[99]
Mali P, Yang L, Esvelt KM, et al. RNA-guided human genome engineering via Cas9. Science 2013; 339(6121): 823-6.
[http://dx.doi.org/10.1126/science.1232033] [PMID: 23287722]
[100]
Nishimasu H, Ran FA, Hsu PD, et al. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 2014; 156(5): 935-49.
[http://dx.doi.org/10.1016/j.cell.2014.02.001] [PMID: 24529477]
[101]
Zhang X-H, Tee LY, Wang XG, Huang QS, Yang SH. Off-target effects in CRISPR/Cas9-mediated genome engineering. Mol Ther Nucleic Acids 2015; 4e264
[http://dx.doi.org/10.1038/mtna.2015.37] [PMID: 26575098]
[102]
Martin F, Sánchez-Hernández S, Gutiérrez-Guerrero A, Pinedo-Gomez J, Benabdellah K. Biased and unbiased methods for the detection of off-target cleavage by CRISPR/Cas9: an overview. Int J Mol Sci 2016; 17(9): 1507.
[http://dx.doi.org/10.3390/ijms17091507] [PMID: 27618019]
[103]
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]
[104]
Anderson KR, Haeussler M, Watanabe C, et al. CRISPR off-target analysis in genetically engineered rats and mice. Nat Methods 2018; 15(7): 512-4.
[http://dx.doi.org/10.1038/s41592-018-0011-5] [PMID: 29786090]
[105]
Yin J, Liu M, Liu Y, et al. Optimizing genome editing strategy by primer-extension-mediated sequencing. Cell Discov 2019; 5(1): 18.
[http://dx.doi.org/10.1038/s41421-019-0088-8] [PMID: 30937179]
[106]
Guilinger JP, Pattanayak V, Reyon D, et al. Broad specificity profiling of TALENs results in engineered nucleases with improved DNA-cleavage specificity. Nat Methods 2014; 11(4): 429-35.
[http://dx.doi.org/10.1038/nmeth.2845] [PMID: 24531420]
[107]
Peng H, Zheng Y, Zhao Z, Liu T, Li J. Recognition of CRISPR/Cas9 off-target sites through ensemble learning of uneven mismatch distributions. Bioinformatics 2018; 34(17): i757-65.
[http://dx.doi.org/10.1093/bioinformatics/bty558] [PMID: 30423065]
[108]
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): 237-43. 1, 243
[http://dx.doi.org/10.1038/nmeth.3284] [PMID: 25664545]
[109]
Huston NC, Tycko J, Tillotson EL, et al. Identification of guide-intrinsic determinants of Cas9 specificity. CRISPR J 2019; 2(3): 172-85.
[http://dx.doi.org/10.1089/crispr.2019.0009] [PMID: 31225747]
[110]
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]
[111]
Mundade R, Ozer HG, Wei H, Prabhu L, Lu T. Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond. Cell Cycle 2014; 13(18): 2847-52.
[http://dx.doi.org/10.4161/15384101.2014.949201] [PMID: 25486472]
[112]
Wienert B, Wyman SK, Richardson CD, et al. Unbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq. Science 2019; 364(6437): 286-9.
[PMID: 31000663]
[113]
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]
[114]
Richardson CD, Ray GJ, Bray NL, Corn JE. Non-homologous DNA increases gene disruption efficiency by altering DNA repair outcomes. Nat Commun 2016; 7(1): 12463.
[http://dx.doi.org/10.1038/ncomms12463] [PMID: 27530320]
[115]
Akcakaya P, Bobbin ML, Guo JA, et al. In vivo CRISPR editing with no detectable genome-wide off-target mutations. Nature 2018; 561(7723): 416-9.
[http://dx.doi.org/10.1038/s41586-018-0500-9] [PMID: 30209390]
[116]
Zischewski J, Fischer R, Bortesi L. Detection of on-target and off-target mutations generated by CRISPR/Cas9 and other sequence-specific nucleases. Biotechnol Adv 2017; 35(1): 95-104.
[http://dx.doi.org/10.1016/j.biotechadv.2016.12.003 PMID: 28011075]
[117]
Paulis M, Castelli A, Lizier M, et al. A pre-screening FISH-based method to detect CRISPR/Cas9 off-targets in mouse embryonic stem cells. Sci Rep 2015; 5(1): 12327.
[http://dx.doi.org/10.1038/srep12327] [PMID: 26204993]
[118]
Zuo E, Sun Y, Wei W, et al. Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos. Science 2019; 364(6437): 289-92.
[http://dx.doi.org/10.1126/science.aav9973] [PMID: 30819928]
[119]
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]
[120]
Frock RL, Hu J, Meyers RM, Ho YJ, 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]
[121]
Kim D, Kim S, Kim S, Park J, Kim JS. Genome-wide target specificities of CRISPR-Cas9 nucleases revealed by multiplex Digenome-seq. Genome Res 2016; 26(3): 406-15.
[http://dx.doi.org/10.1101/gr.199588.115] [PMID: 26786045]
[122]
Crosetto N, Mitra A, Silva MJ, et al. Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing. Nat Methods 2013; 10(4): 361-5.
[http://dx.doi.org/10.1038/nmeth.2408] [PMID: 23503052]
[123]
Cho SW, Kim S, Kim JM, Kim JS. 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]
[124]
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]
[125]
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]
[126]
Dagdas YS, Chen JS, Sternberg SH, Doudna JA, Yildiz A. A conformational checkpoint between DNA binding and cleavage by CRISPR-Cas9. Sci Adv 2017; 3(8)eaao0027
[http://dx.doi.org/10.1126/sciadv.aao0027] [PMID: 28808686]
[127]
Yang M, Peng S, Sun R, Lin J, Wang N, Chen C. The conformational dynamics of Cas9 governing DNA cleavage are revealed by single-molecule FRET. Cell Rep 2018; 22(2): 372-82.
[http://dx.doi.org/10.1016/j.celrep.2017.12.048] [PMID: 29320734]
[128]
Oliveros JC, Franch M, Tabas-Madrid D, et al. Breaking-Cas-interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes. Nucleic Acids Res 2016; 44(W1)W267-71
[http://dx.doi.org/10.1093/nar/gkw407] [PMID: 27166368]
[129]
Winter J, Breinig M, Heigwer F, et al. caRpools: an R package for exploratory data analysis and documentation of pooled CRISPR/Cas9 screens. Bioinformatics 2016; 32(4): 632-4.
[http://dx.doi.org/10.1093/bioinformatics/btv617] [PMID: 26508755]
[130]
Aach J, Mali P, Church GM. CasFinder: Flexible algorithm for identifying specific Cas9 targets in genomes. bioRxiv 2014.005074
[131]
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]
[132]
Ma M, Ye AY, Zheng W, Kong L, et al. A guide RNA sequence design platform for the CRISPR/Cas9 system for model organism genomes. BioMed Res Int 2013; 2013270805
[133]
Park J, Bae S, Kim J-S. Cas-Designer: a web-based tool for choice of CRISPR-Cas9 target sites. Bioinformatics 2015; 31(24): 4014-6.
[http://dx.doi.org/10.1093/bioinformatics/btv537] [PMID: 26358729]
[134]
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]
[135]
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]
[136]
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]
[137]
Heigwer F, Zhan T, Breinig M, et al. CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries. Genome Biol 2016; 17 Article ID 55
[138]
Pulido-Quetglas C, Aparicio-Prat E, Arnan C, et al. Scalable design of paired CRISPR guide RNAs for genomic deletion. PLOS Comput Biol 2017; 13(3)e1005341
[http://dx.doi.org/10.1371/journal.pcbi.1005341] [PMID: 28253259]
[139]
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]
[140]
Pinello L, et al. CRISPResso: sequencing analysis toolbox for CRISPR-Cas9 genome editing. bioRxiv 2015.031203
[141]
Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: A web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic acids research 2007; 35(suppl_2): W52-7.
[http://dx.doi.org/10.1093/nar/gkm360]
[142]
Biswas A, Gagnon JN, Brouns SJ, Fineran PC, Brown CM. CRISPRTarget: bioinformatic prediction and analysis of crRNA targets. RNA Biol 2013; 10(5): 817-27.
[http://dx.doi.org/10.4161/rna.24046] [PMID: 23492433]
[143]
Lindsay H, Burger A, Biyoung B, et al. CrispRVariants: precisely charting the mutation spectrum in genome engineering experiments. bioRxiv 2016.034140
[http://dx.doi.org/10.1038/nbt.3628]
[144]
Prykhozhij SV, Rajan V, Gaston D, Berman JN. CRISPR multitargeter: a web tool to find common and unique CRISPR single guide RNA targets in a set of similar sequences. PLoS One 2015; 10(3)e0119372
[http://dx.doi.org/10.1371/journal.pone.0119372] [PMID: 25742428]
[145]
Hwang G-H, Park J, Lim K, et al. Web-based design and analysis tools for CRISPR base editing. BMC Bioinformatics 2018; 19(1): 542.
[http://dx.doi.org/10.1186/s12859-018-2585-4] [PMID: 30587106]
[146]
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]
[147]
Güell M, Yang L, Church GM. Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA). Bioinformatics 2014; 30(20): 2968-70.
[http://dx.doi.org/10.1093/bioinformatics/btu427] [PMID: 24990609]
[148]
Xie X, Ma X, Zhu Q, Zeng D, Li G, Liu YG. CRISPR-GE: a convenient software toolkit for CRISPR-based genome editing. Mol Plant 2017; 10(9): 1246-9.
[http://dx.doi.org/10.1016/j.molp.2017.06.004] [PMID: 28624544]
[149]
Lei Y, Lu L, Liu HY, Li S, Xing F, Chen LL. 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]
[150]
Minkenberg B, Zhang J, Xie K, Yang Y. CRISPR-PLANT v2: an online resource for highly specific guide RNA spacers based on improved off-target analysis. Plant Biotechnol J 2019; 17(1): 5-8.
[PMID: 30325102]
[151]
Naito Y, Hino K, Bono H, Ui-Tei K. CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites. Bioinformatics 2015; 31(7): 1120-3.
[http://dx.doi.org/10.1093/bioinformatics/btu743] [PMID: 25414360]
[152]
Moreno-Mateos MA, Vejnar CE, Beaudoin JD, 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]
[153]
Zhu LJ, Holmes BR, Aronin N, Brodsky MH. CRISPRseek: a bioconductor package to identify target-specific guide RNAs for CRISPR-Cas9 genome-editing systems. PLoS One 2014; 9(9)e108424
[http://dx.doi.org/10.1371/journal.pone.0108424] [PMID: 25247697]
[154]
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]
[155]
Zhu H, Misel L, Graham M, Robinson ML, Liang C. CT-Finder: A web service for CRISPR optimal target prediction and visualization. Sci Rep 2016; 6(1): 25516.
[http://dx.doi.org/10.1038/srep25516] [PMID: 27210050]
[156]
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]
[157]
Peng D, Tarleton R. EuPaGDT: a web tool tailored to design CRISPR guide RNAs for eukaryotic pathogens. Microb Genom 2015; 1(4)e000033
[http://dx.doi.org/10.1099/mgen.0.000033] [PMID: 28348817]
[158]
Gratz SJ, Ukken FP, Rubinstein CD, et al. Highly specific and efficient CRISPR/Cas9-catalyzed homology-directed repair in Drosophila. Genetics 2014; 196(4): 961-71.
[http://dx.doi.org/10.1534/genetics.113.160713] [PMID: 24478335]
[159]
O’Brien A, Bailey TL. GT-Scan: identifying unique genomic targets. Bioinformatics 2014; 30(18): 2673-5.
[http://dx.doi.org/10.1093/bioinformatics/btu354] [PMID: 24860161]
[160]
Yennmalli R, et al. Computational tools and resources for crispr/cas 9 genome editing method. MOJ Proteom Bioinform 2017; 5(4): 00164.
[161]
Chen W, McKenna A, Schreiber J, et al. Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair. Nucleic Acids Res 2019; 47(15): 7989-8003.
[http://dx.doi.org/10.1093/nar/gkz487] [PMID: 31165867]
[162]
Li W, Xu H, Xiao T, et al. MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biol 2014; 15(12): 554.
[http://dx.doi.org/10.1186/s13059-014-0554-4] [PMID: 25476604]
[163]
Li W, Köster J, Xu H, et al. Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR. Genome Biol 2015; 16(1): 281.
[http://dx.doi.org/10.1186/s13059-015-0843-6] [PMID: 26673418]
[164]
Bae S, Kweon J, Kim HS, Kim JS. Microhomology-based choice of Cas9 nuclease target sites. Nat Methods 2014; 11(7): 705-6.
[http://dx.doi.org/10.1038/nmeth.3015] [PMID: 24972169]
[165]
MacPherson CR, Scherf A. Flexible guide-RNA design for CRISPR applications using Protospacer Workbench. Nat Biotechnol 2015; 33(8): 805-6.
[http://dx.doi.org/10.1038/nbt.3291] [PMID: 26121414]
[166]
Xu H, Xiao T, Chen CH, et al. Sequence determinants of improved CRISPR sgRNA design. Genome Res 2015; 25(8): 1147-57.
[http://dx.doi.org/10.1101/gr.191452.115] [PMID: 26063738]
[167]
Xie S, Shen B, Zhang C, Huang X, Zhang Y. sgRNAcas9: a software package for designing CRISPR sgRNA and evaluating potential off-target cleavage sites. PLoS One 2014; 9(6)e100448
[http://dx.doi.org/10.1371/journal.pone.0100448] [PMID: 24956386]
[168]
Chuai GH, Wang Q-L, Liu Q. In silico meets in vivo: Towards computational CRISPR-based sgRNA design. Trends Biotechnol 2017; 35(1): 12-21.
[http://dx.doi.org/10.1016/j.tibtech.2016.06.008] [PMID: 27418421]
[169]
Chari R, Yeo NC, Chavez A, Church GM. sgRNA Scorer 2.0: a species-independent model to predict CRISPR/Cas9 activity. ACS Synth Biol 2017; 6(5): 902-4.
[http://dx.doi.org/10.1021/acssynbio.6b00343] [PMID: 28146356]
[170]
Upadhyay SK, Sharma S. SSFinder: High throughput CRISPR-Cas target sites prediction tool. BioMed Res Int 2014; 2014Article ID 742482
[171]
Hodgkins A, Farne A, Perera S, et al. WGE: a CRISPR database for genome engineering. Bioinformatics 2015; 31(18): 3078-80.
[http://dx.doi.org/10.1093/bioinformatics/btv308] [PMID: 25979474]
[172]
Hiranniramol K, Chen Y, Liu W, Wang X. Generalizable sgRNA design for improved CRISPR/Cas9 editing efficiency. Bioinformatics 2020; 36(9): 2684-9.
[173]
Chari R, Mali P, Moosburner M, Church GM. Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach. Nat Methods 2015; 12(9): 823-6.
[http://dx.doi.org/10.1038/nmeth.3473] [PMID: 26167643]
[174]
Cong L, Ran FA, Cox D, et al. Multiplex genome engineering using CRISPR/Cas systems. Science 2013; 339(6121): 819-23.
[http://dx.doi.org/10.1126/science.1231143] [PMID: 23287718]
[175]
Koike-Yusa H, Li Y, Tan EP, Velasco-Herrera Mdel C, Yusa K. Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library. Nat Biotechnol 2014; 32(3): 267-73.
[http://dx.doi.org/10.1038/nbt.2800] [PMID: 24535568]
[176]
You Q, Zhong Z, Ren Q, Hassan F, Zhang Y, Zhang T. CRISPRMatch: an automatic calculation and visualization tool for high-throughput CRISPR genome-editing data analysis. Int J Biol Sci 2018; 14(8): 858-62.
[http://dx.doi.org/10.7150/ijbs.24581] [PMID: 29989077]
[177]
Zhou J, Deng K, Cheng Y, et al. CRISPR-Cas9 based genome editing reveals new insights into microRNA function and regulation in rice. Front Plant Sci 2017; 8: 1598.
[http://dx.doi.org/10.3389/fpls.2017.01598] [PMID: 28955376]
[178]
Fusi N, et al. In silico predictive modeling of CRISPR/Cas9 guide efficiency. bioRxiv 2015.021568
[179]
Mendoza BJ, Trinh CT. Enhanced guide-RNA design and targeting analysis for precise CRISPR genome editing of single and consortia of industrially relevant and non-model organisms. Bioinformatics 2018; 34(1): 16-23.
[http://dx.doi.org/10.1093/bioinformatics/btx564] [PMID: 28968798]
[180]
Labuhn M, Adams FF, Ng M, et al. Refined sgRNA efficacy prediction improves large- and small-scale CRISPR-Cas9 applications. Nucleic Acids Res 2018; 46(3): 1375-85.
[http://dx.doi.org/10.1093/nar/gkx1268] [PMID: 29267886]
[181]
Rahman MK, Rahman MS. CRISPRpred: A flexible and efficient tool for sgRNAs on-target activity prediction in CRISPR/Cas9 systems. PLoS One 2017; 12(8)e0181943
[http://dx.doi.org/10.1371/journal.pone.0181943] [PMID: 28767689]
[182]
Kim HK, Min S, Song M, et al. Deep learning improves prediction of CRISPR-Cpf1 guide RNA activity. Nat Biotechnol 2018; 36(3): 239-41.
[http://dx.doi.org/10.1038/nbt.4061] [PMID: 29431740]
[183]
Peng H, Zheng Y, Blumenstein M, Tao D, Li J. CRISPR/Cas9 cleavage efficiency regression through boosting algorithms and Markov sequence profiling. Bioinformatics 2018; 34(18): 3069-77.
[http://dx.doi.org/10.1093/bioinformatics/bty298] [PMID: 29672669]
[184]
Wilson LOW, Reti D, O’Brien AR, Dunne RA, Bauer DC. High activity target-site identification using phenotypic independent CRISPR-Cas9 core functionality. CRISPR J 2018; 1(2): 182-90.
[http://dx.doi.org/10.1089/crispr.2017.0021] [PMID: 31021206]
[185]
Wong N, Liu W, Wang X. WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system. Genome Biol 2015; 16(1): 218.
[http://dx.doi.org/10.1186/s13059-015-0784-0] [PMID: 26521937]
[186]
Housden BE, Valvezan AJ, Kelley C, et al. Identification of potential drug targets for tuberous sclerosis complex by synthetic screens combining CRISPR-based knockouts with RNAi. Sci Signal 2015; 8(393): rs9-9.
[http://dx.doi.org/10.1126/scisignal.aab3729] [PMID: 26350902]
[187]
Zhang D, Hurst T, Duan D, Chen SJ. 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]
[188]
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009; 10(3): R25.
[http://dx.doi.org/10.1186/gb-2009-10-3-r25] [PMID: 19261174]
[189]
Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:13033997 2013.
[190]
Wilson LOW, O’Brien AR, Bauer DC. The current state and future of CRISPR-Cas9 gRNA design tools. Front Pharmacol 2018; 9: 749.
[http://dx.doi.org/10.3389/fphar.2018.00749] [PMID: 30050439]
[191]
Stemmer M, Thumberger T, Del Sol Keyer M, Wittbrodt J, Mateo JL. Correction: CCTop: An intuitive, flexible and reliable CRISPR/Cas9 target prediction tool. PLoS One 2017; 12(4)e0176619
[http://dx.doi.org/10.1371/journal.pone.0176619] [PMID: 28426791]
[192]
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]
[193]
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]
[194]
Xiao A, Cheng Z, Kong L, et al. CasOT: a genome-wide Cas9/gRNA off-target searching tool. Bioinformatics 2014; 30(8): 1180-2.
[http://dx.doi.org/10.1093/bioinformatics/btt764] [PMID: 24389662]
[195]
Jacquin ALS, Odom DT, Lukk M. Crisflash: open-source software to generate CRISPR guide RNAs against genomes annotated with individual variation. Bioinformatics 2019; 35(17): 3146-7.
[http://dx.doi.org/10.1093/bioinformatics/btz019] [PMID: 30649181]
[196]
Odom D, Lukk M, Jacquin ALS. Crisflash: Open-source software to generate CRISPR guide RNAs against genomes annotated with individual variation. Bioinformatics 2019; 35(17): 3146-7.
[197]
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]
[198]
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]
[199]
McKenna A, Shendure J. FlashFry: a fast and flexible tool for large-scale CRISPR target design. BMC Biol 2018; 16(1): 74.
[http://dx.doi.org/10.1186/s12915-018-0545-0] [PMID: 29976198]
[200]
Zhang G, Dai Z, Dai X. C-RNNCrispr: Prediction of CRISPR/Cas9 sgRNA activity using convolutional and recurrent neural networks. Comput Struct Biotechnol J 2020; 18: 344-54.
[http://dx.doi.org/10.1016/j.csbj.2020.01.013] [PMID: 32123556]
[201]
Knight SC, Xie L, Deng W, et al. Dynamics of CRISPR-Cas9 genome interrogation in living cells. Science 2015; 350(6262): 823-6.
[http://dx.doi.org/10.1126/science.aac6572] [PMID: 26564855]
[202]
Chen F, Ding X, Feng Y, Seebeck T, Jiang Y, Davis GD. Targeted activation of diverse CRISPR-Cas systems for mammalian genome editing via proximal CRISPR targeting. Nat Commun 2017; 8: 14958.
[http://dx.doi.org/10.1038/ncomms14958] [PMID: 28387220]
[203]
Isaac RS, Jiang F, Doudna JA, Lim WA, Narlikar GJ, Almeida R. Nucleosome breathing and remodeling constrain CRISPR-Cas9 function. eLife 2016; 5e13450
[http://dx.doi.org/10.7554/eLife.13450] [PMID: 27130520]
[204]
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]
[205]
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]
[206]
Horlbeck MA, Witkowsky LB, Guglielmi B, et al. Nucleosomes impede Cas9 access to DNA in vivo and in vitro. eLife 2016; 5e12677
[http://dx.doi.org/10.7554/eLife.12677]
[207]
Yao X, Wang X, Hu X, et al. Homology-mediated end joining-based targeted integration using CRISPR/Cas9. Cell Res 2017; 27(6): 801-14.
[http://dx.doi.org/10.1038/cr.2017.76] [PMID: 28524166]
[208]
Merkle FT, Neuhausser WM, Santos D, et al. Efficient CRISPR-Cas9-mediated generation of knockin human pluripotent stem cells lacking undesired mutations at the targeted locus. Cell Rep 2015; 11(6): 875-83.
[http://dx.doi.org/10.1016/j.celrep.2015.04.007] [PMID: 25937281]
[209]
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]

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