Development of CRISPR/Cas9 system for targeted DNA modifications and recent improvements in modification efficiency and specificity

다국어 초록 (Multilingual Abstract)

The targeted nuclease clustered, regularly interspaced short palindromic repeats/CRISPR-associated proteins (CRISPR/Cas) system has recently emerged as a prominent gene manipulation method. Because of its ease in programming targeted DNA/protein binding through RNA in a vast range of organisms, this prokaryotic defense system is a versatile tool with many applications in the research field as well as high potential in agricultural and clinical improvements. This review will present a brief history that led to its discovery and adaptation.
We also present some of its restrictions, and modifications that have been performed to overcome such restrictions, focusing specifically on the most common CRISPR/Cas9 mediated non-homologous end joint repair.

참고문헌 (Reference)

1 Zhu Y, "qDSB-Seq is a general method for genome-wide quantification of DNA double-strand breaks using sequencing" 10 : 1-11, 2019

2 Karvelis T, "crRNA and tracrRNA guide Cas9-mediated DNA interference in Streptococcus thermophilus" 10 : 841-851, 2013

3 Grunewald J, "Transcriptome-wide off-target RNA editing induced by CRISPRguided DNA base editors" 569 : 433-437, 2019

4 Mojica FJ, "Transcription at different salinities of Haloferax mediterranei sequences adjacent to partially modified PstI sites" 9 : 613-621, 1993

5 Pickar-Oliver A, "The next generation of CRISPR-Cas technologies and applications" 20 : 490-507, 2019

6 Lieber MR, "The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway" 79 : 181-211, 2010

7 Sapranauskas R, "The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli" 39 : 9275-9282, 2011

8 Garneau JE, "The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA" 468 : 67-71, 2010

9 Cyranoski D, "The CRISPR-baby scandal : what's next for human gene-editing" 566 : 440-442, 2019

10 Christian M, "Targeting DNA double-strand breaks with TAL effector nucleases" 186 : 757-761, 2010

11 Cho SW, "Targeted genome engineering in human cells with the Cas9RNA-guided endonuclease" 31 : 230-232, 2013

12 Winter J, "Targeted exon skipping with AAV-mediated split adenine base editors" 5 : 1-12, 2019

13 Anders C, "Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease" 513 : 569-573, 2014

14 Nambiar TS, "Stimulation of CRISPR-mediated homology-directed repair by an engineered RAD18 variant" 10 : 3395-, 2019

15 Wang Y, "Specificity profiling of CRISPR system reveals greatly enhanced off-target gene editing" 10 : 1-8, 2020

16 Brouns SJ, "Small CRISPR RNAs guide antiviral defense in prokaryotes" 321 : 960-964, 2008

17 Kim YG, "Site-specific cleavage of DNA-RNA hybrids by zinc finger/FokI cleavage domain fusions" 203 : 43-49, 1997

18 Choo Y, "Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions" 91 : 11168-11172, 1994

19 Anzalone AV, "Search-and-replace genome editing without double-strand breaks or donor DNA" 576 : 149-157, 2019

20 Doench JG, "Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation" 32 : 1262-1267, 2014

21 Jinek M, "RNA-programmed genome editing in human cells" 2 : e00471-, 2013

22 Mali P, "RNA-guided human genome engineering via Cas9" 339 : 823-826, 2013

23 Cencic R, "Protospacer adjacent motif(PAM)-distal sequences engage CRISPR Cas9 DNA target cleavage" 9 : e109213-, 2014

24 El-Mounadi K, "Principles, Applications, and Biosafety of Plant Genome Editing Using CRISPR-Cas9" 11 : 56-, 2020

25 Deveau H, "Phage response to CRISPR-encoded resistance in Streptococcus thermophilus" 190 : 1390-1400, 2008

26 Zhang XH, "Off-target effects in CRISPR/Cas9-mediated genome engineering" 4 : e264-, 2015

27 Ishino Y, "Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product" 169 : 5429-5433, 1987

28 Brogna S, "Nonsense-mediated mRNA decay(NMD)mechanisms" 16 : 107-113, 2009

29 Seligman LM, "Mutations altering the cleavage specificity of a homing endonuclease" 30 : 3870-3879, 2002

30 Cong L, "Multiplex genome engineering using CRISPR/Cas systems" 339 : 819-823, 2013

31 Vasquez KM, "Manipulating the mammalian genome by homologous recombination" 98 : 8403-8410, 2001

32 Popp MW, "Leveraging rules of nonsense-mediated mRNA decay for genome engineering and personalized medicine" 165 : 1319-1322, 2016

33 Sussman D, "Isolation and characterization of new homing endonuclease specificities at individual target site positions" 342 : 31-41, 2004

34 Mojica FJ, "Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements" 60 : 174-182, 2005

35 Smithies O, "Insertion of DNA sequences into the human chromosomal beta-globin locus by homologous recombination" 317 : 230-234, 1985

36 Jansen R, "Identification of genes that are associated with DNA repeats in prokaryotes" 43 : 1565-1575, 2002

37 Kim YG, "Hybrid restriction enzymes : zinc finger fusions to Fok I cleavage domain" 93 : 1156-1160, 1996

38 Bollag RJ, "Homologous recombination in mammalian cells" 23 : 199-225, 1989

39 Chevalier BS, "Homing endonucleases : structural and functional insight into the catalysts of intron/intein mobility" 29 : 3757-3774, 2001

40 Rosen LE, "Homing endonuclease I-CreI derivatives with novel DNA target specificities" 34 : 4791-4800, 2006

41 Kim S, "Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins" 24 : 1012-1019, 2014

42 Fu Y, "High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells" 31 : 822-826, 2013

43 Mirzazadeh R, "Genome-wide profiling of DNA double-strand breaks by the BLESS and BLISS methods" 1672 : 167-194, 2018

44 Wu X, "Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells" 32 : 670-676, 2014

45 Kuscu C, "Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease" 32 : 677-683, 2014

46 Urnov FD, "Genome editing with engineered zinc finger nucleases" 11 : 636-646, 2010

47 Wang T, "Genetic screens in human cells using the CRISPR-Cas9system" 343 : 80-84, 2014

48 Kim Y, "Generation of knockout mice by Cpf1-mediated gene targeting" 34 : 808-810, 2016

49 Bouabe H, "Gene targeting in mice : a review" 1064 : 315-336, 2013

50 Tsai SQ, "GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases" 33 : 187-197, 2015

51 Li L, "Functional domains in Fok I restriction endonuclease" 89 : 4275-4279, 1992

52 Rouet P, "Expression of a site-specific endonuclease stimulates homologous recombination in mammalian cells" 91 : 6064-6068, 1994

53 Bibikova M, "Enhancing gene targeting with designed zinc finger nucleases" 300 : 764-, 2003

54 Gagnon JA, "Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs" 9 : e98186-, 2014

55 Koonin EV, "Diversity, classification and evolution of CRISPR-Cas systems" 37 : 67-78, 2017

56 Horvath P, "Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus" 190 : 1401-1412, 2008

57 Kim D, "Digenome-seq : genome-wide profiling of CRISPR-Cas9 off-target effects in human cells" 12 : 237-243, 2015

58 Hsu PD, "DNA targeting specificity of RNA-guided Cas9 nucleases" 31 : 827-832, 2013

59 Zetsche B, "Cpf1 is a single RNA-guided endonuclease of a class 2CRISPR-Cas system" 163 : 759-771, 2015

60 Carroll D, "Collateral damage : benchmarking off-target effects in genome editing" 20 : 114-, 2019

61 Bolotin A, "Clustered regularly interspaced short palindrome repeats(CRISPRs)have spacers of extrachromosomal origin" 151 : 2551-2561, 2005

62 Makarova KS, "Classification and nomenclature of CRISPR-Cas systems: where from here?" 1 : 325-336, 2018

63 Gasiunas G, "Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria" 109 : E2579-2586, 2012

64 Singh R, "Cas9-chromatin binding information enables more accurate CRISPR off-target prediction" 43 : e118-, 2015

65 Tuladhar R, "CRISPRCas9-based mutagenesis frequently provokes on-target mRNA misregulation" 10 : 4056-, 2019

66 Chen D, "CRISPR/Cas9-mediated genome editing induces exon skipping by complete or stochastic altering splicing in the migratory locust" 18 : 1-9, 2018

67 Mou H, "CRISPR/Cas9-mediated genome editing induces exon skipping by alternative splicing or exon deletion" 18 : 1-8, 2017

68 Sui T, "CRISPR-induced exon skipping is dependent on premature termination codon mutations" 19 : 164-, 2018

69 Paul B, "CRISPR-Cas12a : Functional overview and applications" 43 : 8-17, 2020

70 Cebrian-Serrano A, "CRISPR-Cas orthologues and variants : optimizing the repertoire, specificity and delivery of genome engineering tools" 28 : 247-261, 2017

71 Sorek R, "CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea" 6 : 181-186, 2008

72 Barrangou R, "CRISPR provides acquired resistance against viruses in prokaryotes" 315 : 1709-1712, 2007

73 Wienert B, "CRISPR off-target detection with DISCOVER-seq" 15 : 1775-1799, 2020

74 Marraffini LA, "CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA" 322 : 1843-1845, 2008

75 Pourcel C, "CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies" 151 : 653-663, 2005

76 Deltcheva E, "CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III" 471 : 602-607, 2011

77 Grunewald J, "CRISPR DNA base editors with reduced RNA off-target and self-editing activities" 37 : 1041-1048, 2019

78 Mali P, "CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering" 31 : 833-838, 2013

79 Boch J, "Breaking the code of DNA binding specificity of TAL-type III effectors" 326 : 1509-1512, 2009

80 Wright AV, "Biology and applications of CRISPR systems : Harnessing Nature's Toolbox for Genome Engineering" 164 : 29-44, 2016

81 Mojica FJ, "Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria" 36 : 244-246, 2000

82 Lassoued R, "Benefits of genome-edited crops : expert opinion" 28 : 247-256, 2019

83 Rees HA, "Base editing : precision chemistry on the genome and transcriptome of living cells" 19 : 770-788, 2018

84 Cho SW, "Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases" 24 : 132-141, 2014

85 Makarova KS, "An updated evolutionary classification of CRISPR-Cas systems" 13 : 722-736, 2015

86 Jinek M, "A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity" 337 : 816-821, 2012