The Conspicuity of CRISPR-Cpf1 System as a Significant Breakthrough in Genome Editing

Current Microbiology

Volumn 75, Issue 1, 2018, Pages 107-115

  Bayat, Hadi ^a,b   Modarressi, Mohammad Hossein ^c   Rahimpour, Azam ^a,b  

^a SHAHID BEHESHTI UNIVERSITY OF MEDICAL SCIENCES   (Iran)

^b SHAHID BEHESHTI UNIVERSITY OF MEDICAL SCIENCES   (Iran)

^c TEHRAN UNIVERSITY OF MEDICAL SCIENCES   (Iran)

Author keywords

[No Author keywords available]

Indexed keywords

CALCIUM ION; CPF1 PROTEIN; MAGNESIUM ION; MEMBRANE PROTEIN; MESSENGER RNA; MICRORNA; RIBONUCLEASE; UNCLASSIFIED DRUG; BACTERIAL PROTEIN; ENDONUCLEASE;

BINDING AFFINITY; CRISPR CAS SYSTEM; DNA CLEAVAGE; ENZYME ACTIVITY; GENE EDITING; GENE EXPRESSION; GENE SEQUENCE; GENETIC TRANSFECTION; GENOME; HUMAN; MUTAGENESIS; NONHUMAN; REVIEW; BACTERIUM; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; ENZYMOLOGY; GENETICS; METABOLISM;

BACTERIA; BACTERIAL PROTEINS; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; ENDONUCLEASES; GENE EDITING;

EID: 85035805931     PISSN: 03438651     EISSN: 14320991     Source Type: Journal    
DOI: 10.1007/s00284-017-1406-8     Document Type: Review

References (79)

1. Alcon P, Montoya G, Stella S (2017) Assembly of Francisella novicida Cpf1 endonuclease in complex with guide RNA and target DNA. Acta Crystallogr F 73(Pt 7):409–415. https://doi.org/10.1107/S2053230X1700838X
2. Bae S, Park J, Kim JS (2014) Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 30(10):1473–1475. https://doi.org/10.1093/bioinformatics/btu048
3. Bayat H, Omidi M, Rajabibazl M, Sabri S, Rahimpour A (2017) The CRISPR growth spurt: from bench to clinic on versatile small RNAs. J Microbiol Biotechnol 27(2):207–218. https://doi.org/10.4014/jmb.1607.07005
4. Charpentier E, Richter H, van der Oost J, White MF (2015) Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity. FEMS Microbiol Rev 39(3):428–441. https://doi.org/10.1093/femsre/fuv023
5. Chira S, Gulei D, Hajitou A, Zimta AA, Cordelier P, Berindan-Neagoe I (2017) CRISPR/Cas9: transcending the reality of genome editing. Mol Ther Nucleic Acids 7:211–222. https://doi.org/10.1016/j.omtn.2017.04.001
6. Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, Eckert MR, Vogel J, Charpentier E (2011) CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471(7340):602–607. https://doi.org/10.1038/nature09886
7. Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, Smith I, Tothova Z, Wilen C, Orchard R, Virgin HW, Listgarten J, Root DE (2016) Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol. https://doi.org/10.1038/nbt.3437
8. Dong D, Ren K, Qiu X, Zheng J, Guo M, Guan X, Liu H, Li N, Zhang B, Yang D, Ma C, Wang S, Wu D, Ma Y, Fan S, Wang J, Gao N, Huang Z (2016) The crystal structure of Cpf1 in complex with CRISPR RNA. Nature 532(7600):522–526. https://doi.org/10.1038/nature17944
9. Doudna JA, Charpentier E (2014) Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 346(6213):1258096. https://doi.org/10.1126/science.1258096
10. Dow LE (2015) Modeling disease in vivo with CRISPR/Cas9. Trends Mol Med 21(10):609–621. https://doi.org/10.1016/j.molmed.2015.07.006
11. Eggeling L, Bott M (2015) A giant market and a powerful metabolism: L-lysine provided by Corynebacterium glutamicum. Appl Microbiol Biotechnol 99(8):3387–3394. https://doi.org/10.1007/s00253-015-6508-2
12. Esvelt KM, Mali P, Braff JL, Moosburner M, Yaung SJ, Church GM (2013) Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat Methods 10(11):1116–1121. https://doi.org/10.1038/nmeth.2681
13. Fagerlund RD, Staals RH, Fineran PC (2015) The Cpf1 CRISPR-Cas protein expands genome-editing tools. Genome Biol 16:251. https://doi.org/10.1186/s13059-015-0824-9
14. Fellmann C, Gowen BG, Lin PC, Doudna JA, Corn JE (2017) Cornerstones of CRISPR-Cas in drug discovery and therapy. Nat Rev Drug Discov 16(2):89–100. https://doi.org/10.1038/nrd.2016.238
15. Fonfara I, Richter H, Bratovic M, Le Rhun A, Charpentier E (2016) The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA. Nature. https://doi.org/10.1038/nature17945
16. Fu Y, Sander JD, Reyon D, Cascio VM, Joung JK (2014) Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol 32:279–284. https://doi.org/10.1038/nbt.2808
17. Gao L, Cox DBT, Yan WX, Manteiga JC, Schneider MW, Yamano T, Nishimasu H, Nureki O, Crosetto N, Zhang F (2017) Engineered Cpf1 variants with altered PAM specificities. Nat Biotechnol. https://doi.org/10.1038/nbt.3900
18. Gao P, Yang H, Rajashankar KR, Huang Z, Patel DJ (2016) Type V CRISPR-Cas Cpf1 endonuclease employs a unique mechanism for crRNA-mediated target DNA recognition. Cell Res 26(8):901–913. https://doi.org/10.1038/cr.2016.88
19. Haeussler M, Schonig K, Eckert H, Eschstruth A, Mianne J, Renaud JB, Schneider-Maunoury S, Shkumatava A, Teboul L, Kent J, Joly JS, Concordet JP (2016) Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol 17(1):148. https://doi.org/10.1186/s13059-016-1012-2
20. Haurwitz RE, Jinek M, Wiedenheft B, Zhou K, Doudna JA (2010) Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science 329(5997):1355–1358. https://doi.org/10.1126/science.1192272
21. Heider SA, Wendisch VF (2015) Engineering microbial cell factories: metabolic engineering of Corynebacterium glutamicum with a focus on non-natural products. Biotechnol J 10(8):1170–1184. https://doi.org/10.1002/biot.201400590
22. Horvath P, Romero DA, Coute-Monvoisin AC, Richards M, Deveau H, Moineau S, Boyaval P, Fremaux C, Barrangou R (2008) Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. J Bacteriol 190(4):1401–1412. https://doi.org/10.1128/JB.01415-07
23. Hur JK, Kim K, Been KW, Baek G, Ye S, Hur JW, Ryu SM, Lee YS, Kim JS (2016) Targeted mutagenesis in mice by electroporation of Cpf1 ribonucleoproteins. Nat Biotechnol 34(8):807–808. https://doi.org/10.1038/nbt.3596
24. Jiang Y, Qian F, Yang J, Liu Y, Dong F, Xu C, Sun B, Chen B, Xu X, Li Y, Wang R, Yang S (2017) CRISPR-Cpf1 assisted genome editing of Corynebacterium glutamicum. Nat Commun 8:15179. https://doi.org/10.1038/ncomms15179
25. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337(6096):816–821. https://doi.org/10.1126/science.1225829
26. Jinek M, Jiang F, Taylor DW, Sternberg SH, Kaya E, Ma E, Anders C, Hauer M, Zhou K, Lin S, Kaplan M, Iavarone AT, Charpentier E, Nogales E, Doudna JA (2014) Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 343(6176):1247997. https://doi.org/10.1126/science.1247997
27. Karvelis T, Gasiunas G, Young J, Bigelyte G, Silanskas A, Cigan M, Siksnys V (2015) Rapid characterization of CRISPR-Cas9 protospacer adjacent motif sequence elements. Genome Biol 16:253. https://doi.org/10.1186/s13059-015-0818-7
28. Kato T, Takada S (2017) In vivo and in vitro disease modeling with CRISPR/Cas9. Brief Funct Genomics 16(1):13–24. https://doi.org/10.1093/bfgp/elw031
29. Kennedy EM, Cullen BR (2015) Bacterial CRISPR/Cas DNA endonucleases: a revolutionary technology that could dramatically impact viral research and treatment. Virology 479–480:213–220. https://doi.org/10.1016/j.virol.2015.02.024
30. Kim D, Kim S, Kim S, Park J, Kim JS (2016) Genome-wide target specificities of CRISPR-Cas9 nucleases revealed by multiplex Digenome-sEq. Genome Res 26(3):406–415. https://doi.org/10.1101/gr.199588.115
31. Kim D, Kim J, Hur JK, Been KW, Yoon SH, Kim JS (2016) Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells. Nat Biotechnol 34(8):863–868. https://doi.org/10.1038/nbt.3609
32. Kim D, Bae S, Park J, Kim E, Kim S, Yu HR, Hwang J, Kim JI, Kim JS (2015) Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells. Nat Methods 12(3):237–243. https://doi.org/10.1038/nmeth.3284 (231 p following 243)
33. Kim H, Kim ST, Ryu J, Kang BC, Kim JS, Kim SG (2017) CRISPR/Cpf1-mediated DNA-free plant genome editing. Nat Commun 8:14406. https://doi.org/10.1038/ncomms14406
34. Kim HK, Song M, Lee J, Menon AV, Jung S, Kang YM, Choi JW, Woo E, Koh HC, Nam JW, Kim H (2017) In vivo high-throughput profiling of CRISPR-Cpf1 activity. Nat Methods 14(2):153–159. https://doi.org/10.1038/nmeth.4104
35. Kim K, Park SW, Kim JH, Lee SH, Kim D, Koo T, Kim KE, Kim JH, Kim JS (2017) Genome surgery using Cas9 ribonucleoproteins for the treatment of age-related macular degeneration. Genome Res 27(3):419–426. https://doi.org/10.1101/gr.219089.116
36. Kim SK, Kim H, Ahn WC, Park KH, Woo EJ, Lee DH, Lee SG (2017) Efficient transcriptional gene repression by type V-A CRISPR-Cpf1 from Eubacterium eligens. ACS Synth Biol. https://doi.org/10.1021/acssynbio.6b00368
37. Kim Y, Cheong SA, Lee JG, Lee SW, Lee MS, Baek IJ, Sung YH (2016) Generation of knockout mice by Cpf1-mediated gene targeting. Nat Biotechnol 34(8):808–810. https://doi.org/10.1038/nbt.3614
38. Kleinstiver B, Prew M, Tsai S, Topkar V, Nguyen N, Zheng Z (2015) Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature 523:4
39. Kleinstiver BP, Pattanayak V, Prew MS, Nguyen QS, Zheng NT, Joung Z JK (2016) High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects. Nature. https://doi.org/10.1038/nature16526
40. Kleinstiver BP, Tsai SQ, Prew MS, Nguyen NT, Welch MM, Lopez JM, McCaw ZR, Aryee MJ, Joung JK (2016) Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells. Nat Biotechnol 34(8):869–874. https://doi.org/10.1038/nbt.3620
41. Komor AC, Badran AH, Liu DR (2017) CRISPR-based technologies for the manipulation of eukaryotic genomes. Cell 168(1–2):20–36. https://doi.org/10.1016/j.cell.2016.10.044
42. Labun K, Montague TG, Gagnon JA, Thyme SB, Valen E (2016) CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering. Nucleic Acids Res 44(W1):W272–W276. https://doi.org/10.1093/nar/gkw398
43. Lei C, Li SY, Liu JK, Zheng X, Zhao GP, Wang J (2017) The CCTL (Cpf1-assisted Cutting and Taq DNA ligase-assisted Ligation) method for efficient editing of large DNA constructs in vitro. Nucleic Acids Res 45(9):e74. https://doi.org/10.1093/nar/gkx018
44. Li B, Zhao W, Luo X, Zhang X, Li C, Zeng C, Dong Y (2017) Engineering CRISPR-Cpf1 crRNAs and mRNAs to maximize genome editing efficiency. Nat Biomed Eng. https://doi.org/10.1038/s41551-017-0066
45. Mohanraju P, Makarova KS, Zetsche B, Zhang F, Koonin EV, van der Oost J (2016) Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems. Science 353(6299):aad5147. https://doi.org/10.1126/science.aad5147
46. Nam KH, Haitjema C, Liu X, Ding F, Wang H, DeLisa MP, Ke A (2012) Cas5d protein processes pre-crRNA and assembles into a cascade-like interference complex in subtype I-C/Dvulg CRISPR-Cas system. Structure 20(9):1574–1584. https://doi.org/10.1016/j.str.2012.06.016
47. Nishimasu H, Yamano T, Gao L, Zhang F, Ishitani R, Nureki O (2017) Structural basis for the altered PAM recognition by engineered CRISPR-Cpf1. Mol Cell. https://doi.org/10.1016/j.molcel.2017.04.019
48. Okibe N, Suzuki N, Inui M, Yukawa H (2011) Efficient markerless gene replacement in Corynebacterium glutamicum using a new temperature-sensitive plasmid. J Microbiol Methods 85(2):155–163. https://doi.org/10.1016/j.mimet.2011.02.012
49. Qi L, Larson M, Gilbert L, Doudna J, Weissman J, Arkin A, Lim W (2013) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152(5):10. https://doi.org/10.1016/j.cell.2013.02.022
50. Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F (2013) Genome engineering using the CRISPR-Cas9 system. Nat Protoc 8(11):28. https://doi.org/10.1038/nprot.2013.143
51. Ran FA, Hsu PD, Lin CY, Gootenberg JS, Konermann S, Trevino AE, Scott DA, Inoue A, Matoba S, Zhang Y, Zhang F (2013) Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154(6):1380–1389. https://doi.org/10.1016/j.cell.2013.08.021
52. Ran FA, Cong L, Yan WX, Scott DA, Gootenberg JS, Kriz AJ, Zetsche B, Shalem O, Wu X, Makarova KS, Koonin EV, Sharp PA, Zhang F (2015) In vivo genome editing using Staphylococcus aureus Cas9. Nature 520(7546):186–191. https://doi.org/10.1038/nature14299
53. Slaymaker IM, Gao L, Zetsche B, Scott DA, Yan WX, Zhang F (2016) Rationally engineered Cas9 nucleases with improved specificity. Science 351(6268):84–88. https://doi.org/10.1126/science.aad5227
54. Stella S, Alcon P, Montoya G (2017) Structure of the Cpf1 endonuclease R-loop complex after target DNA cleavage. Nature 546(7659):559–563. https://doi.org/10.1038/nature22398
55. Stemmer M, Thumberger T, Del Sol Keyer M, Wittbrodt J, Mateo JL (2015) CCTop: an intuitive, flexible and reliable CRISPR/Cas9 target prediction tool. PLoS ONE 10(4):e0124633. https://doi.org/10.1371/journal.pone.0124633
56. Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA (2014) DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507(7490):62–67. https://doi.org/10.1038/nature13011
57. Szczelkun MD, Tikhomirova MS, Sinkunas T, Gasiunas G, Karvelis T, Pschera P, Siksnys V, Seidel R (2014) Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes. Proc Natl Acad Sci USA 111(27):9798–9803. https://doi.org/10.1073/pnas.1402597111
58. Tang X, Lowder LG, Zhang T, Malzahn AA, Zheng X, Voytas DF, Zhong Z, Chen Y, Ren Q, Li Q, Kirkland ER, Zhang Y, Qi Y (2017) A CRISPR-Cpf1 system for efficient genome editing and transcriptional repression in plants. Nat Plants 3:17018. https://doi.org/10.1038/nplants.2017.18
59. Toth E, Weinhardt N, Bencsura P, Huszar K, Kulcsar PI, Talas A, Fodor E, Welker E (2016) Cpf1 nucleases demonstrate robust activity to induce DNA modification by exploiting homology directed repair pathways in mammalian cells. Biol Direct 11:46. https://doi.org/10.1186/s13062-016-0147-0
60. Tsai SQ, Zheng Z, Nguyen NT, Liebers M, Topkar VV, Thapar V, Wyvekens N, Khayter C, Iafrate AJ, Le LP, Aryee MJ, Joung JK (2015) GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol 33(2):187–197. https://doi.org/10.1038/nbt.3117
61. Tu M, Lin L, Cheng Y, He X, Sun H, Xie H, Fu J, Liu C, Li J, Chen D, Xi H, Xue D, Liu Q, Zhao J, Gao C, Song Z, Qu J, Gu F (2017) A ‘new lease of life’: FnCpf1 possesses DNA cleavage activity for genome editing in human cells. Nucleic Acids Res. https://doi.org/10.1093/nar/gkx783
62. Ungerer J, Pakrasi HB (2016) Cpf1 is a versatile tool for CRISPR genome editing across diverse species of cyanobacteria. Sci Rep 6:39681. https://doi.org/10.1038/srep39681
63. Wendisch VF, Jorge JMP, Perez-Garcia F, Sgobba E (2016) Updates on industrial production of amino acids using Corynebacterium glutamicum. World J Microbiol Biotechnol 32(6):105. https://doi.org/10.1007/s11274-016-2060-1
64. White MF (2016) Cpf1 shape-shifts for streamlined CRISPR cleavage. Nat Struct Mol Biol 23(5):365–366. https://doi.org/10.1038/nsmb.3225
65. Xu R, Qin R, Li H, Li D, Li L, Wei P, Yang J (2017) Generation of targeted mutant rice using a CRISPR-Cpf1 system. Plant Biotechnol J 15(6):713–717. https://doi.org/10.1111/pbi.12669
66. Yamano T, Zetsche B, Ishitani R, Zhang F, Nishimasu H, Nureki O (2017) Structural basis for the canonical and non-canonical PAM recognition by CRISPR-Cpf1. Mol Cell 67(4):633–645 e633. https://doi.org/10.1016/j.molcel.2017.06.035
67. Yamano T, Nishimasu H, Zetsche B, Hirano H, Slaymaker IM, Li Y, Fedorova I, Nakane T, Makarova KS, Koonin EV, Ishitani R, Zhang F, Nureki O (2016) Crystal structure of Cpf1 in complex with guide RNA and target DNA. Cell 165(4):949–962. https://doi.org/10.1016/j.cell.2016.04.003
68. Yan MY, Yan HQ, Ren GX, Zhao JP, Guo XP, Sun YC (2017) CRISPR-Cas12a-assisted recombineering in bacteria. Appl Environ Microbiol 83 (17). https://doi.org/10.1128/AEM.00947-17
69. Yang M, Wei H, Wang Y, Deng J, Tang Y, Zhou L, Guo G, Tong A (2017) Targeted disruption of V600E-mutant BRAF gene by CRISPR-Cpf1. Mol Ther Nucleic Acids 8:450–458. https://doi.org/10.1016/j.omtn.2017.05.009
70. Zaidi SS, Mahfouz MM, Mansoor S (2017) CRISPR-Cpf1: a new tool for plant genome editing. Trends Plant Sci 22(7):550–553. https://doi.org/10.1016/j.tplants.2017.05.001
71. Zetsche B, Strecker J, Abudayyeh OO, Gootenberg JS, Scott DA, Zhang F (2017) A survey of genome editing activity for 16 Cpf1 orthologs. bioRxiv. https://doi.org/10.1101/134015
72. Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A, Koonin EV, Zhang F (2015) Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163(3):759–771. https://doi.org/10.1016/j.cell.2015.09.038
73. Zetsche B, Heidenreich M, Mohanraju P, Fedorova I, Kneppers J, DeGennaro EM, Winblad N, Choudhury SR, Abudayyeh OO, Gootenberg JS, Wu WY, Scott DA, Severinov K, van der Oost J, Zhang F (2017) Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array. Nat Biotechnol 35(1):31–34. https://doi.org/10.1038/nbt.3737
74. Zhang X, Wang J, Cheng Q, Zheng X, Zhao G, Wang J (2017) Multiplex gene regulation by CRISPR-ddCpf1. Cell Discov 3:17018. https://doi.org/10.1038/celldisc.2017.18
75. Zhang Y, Rajan R, Seifert HS, Mondragon A, Sontheimer EJ (2015) DNase H activity of Neisseria meningitidis Cas9. Mol Cell 60(2):242–255. https://doi.org/10.1016/j.molcel.2015.09.020
76. Zhang Y, Heidrich N, Ampattu BJ, Gunderson CW, Seifert HS, Schoen C, Vogel J, Sontheimer EJ (2013) Processing-independent CRISPR RNAs limit natural transformation in Neisseria meningitidis. Mol Cell 50(4):488–503. https://doi.org/10.1016/j.molcel.2013.05.001
77. Zhang Y, Long C, Li H, McAnally JR, Baskin KK, Shelton JM, Bassel-Duby R, Olson EN (2017) CRISPR-Cpf1 correction of muscular dystrophy mutations in human cardiomyocytes and mice. Sci Adv 3(4):e1602814. https://doi.org/10.1126/sciadv.1602814
78. Zhang Y, Ge X, Yang F, Zhang L, Zheng J, Tan X, Jin ZB, Qu J, Gu F (2014) Comparison of non-canonical PAMs for CRISPR/Cas9-mediated DNA cleavage in human cells. Sci Rep 4:5405. https://doi.org/10.1038/srep05405
79. Zhong G, Wang H, Li Y, Tran MH, Farzan M (2017) Cpf1 proteins excise CRISPR RNAs from mRNA transcripts in mammalian cells. Nat Chem Biol. https://doi.org/10.1038/nchembio.2410