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Protein & Cell

ISSN 1674-800X

ISSN 1674-8018(Online)

CN 11-5886/Q

Postal Subscription Code 80-984

2018 Impact Factor: 7.575

Protein Cell    2020, Vol. 11 Issue (9) : 624-629    https://doi.org/10.1007/s13238-020-00708-8
COMMENTARY
The expanded development and application of CRISPR system for sensitive nucleotide detection
Fengjing Jia1, Xuewen Li4, Chao Zhang1(), Xueming Tang2,3()
1. Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200000, China
2. Institute of Biotechnology Research, Shanghai Academy of Agricultural Sciences, Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
3. Crops Ecological Environment Security Inspection and Supervision Center (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
4. Silicon Gene Tech Co., Ltd., Shanghai 200124, China
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Corresponding Author(s): Chao Zhang,Xueming Tang   
Online First Date: 14 September 2020    Issue Date: 25 September 2020
 Cite this article:   
Fengjing Jia,Xuewen Li,Chao Zhang, et al. The expanded development and application of CRISPR system for sensitive nucleotide detection[J]. Protein Cell, 2020, 11(9): 624-629.
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https://academic.hep.com.cn/pac/EN/10.1007/s13238-020-00708-8
https://academic.hep.com.cn/pac/EN/Y2020/V11/I9/624
1 OO Abudayyeh, JS Gootenberg, S Konermann, J Joung, IM Slaymaker, DB Cox, S Shmakov, KS Makarova, E Semenova, L Minakhinet al. (2016) C2c2 is a single-component programmable RNAguided RNA-targeting CRISPR effector. Science 353:aaf5573
https://doi.org/10.1126/science.aaf5573
2 OO Abudayyeh, JS Gootenberg, MJ Kellner, F Zhang (2019) Nucleic acid detection of plant genes using CRISPR-Cas13. CRISPR J 2:165–171
https://doi.org/10.1089/crispr.2019.0011
3 AV Anzalone, PB Randolph, JR Davis, AA Sousa, LW Koblan, JM Levy, PJ Chen, C Wilson, GA Newby, A Raguramet al. (2019) Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576:149–157
https://doi.org/10.1038/s41586-019-1711-4
4 R Barrangou, A Marraffini Luciano (2014) CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity. Mol Cell 54:234–244
https://doi.org/10.1016/j.molcel.2014.03.011
5 W Chang, W, Liu Y Liu, F Zhan, H Chen, H, Lei Y Liu (2019) Colorimetric detection of nucleic acid sequences in plant pathogens based on CRISPR/Cas9 triggered signal amplification. Microchim Acta 186:243
https://doi.org/10.1007/s00604-019-3348-2
6 JS Chen, E Ma, LB Harrington, M Da Costa, X Tian, JM Palefsky, JA Doudna (2018) CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science 360:436–439
https://doi.org/10.1126/science.aar6245
7 A East-Seletsky , MR O’Connell, SC Knight, D Burstein, JH Cate, R Tjian, JA Doudna (2016) Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature 538:270–273
https://doi.org/10.1038/nature19802
8 AE Field, N Robertson, T Wang, A Havas, T Ideker, PD Adams (2018) DNA methylation clocks in aging: categories, causes, and consequences. Mol Cell 71:882–895
https://doi.org/10.1016/j.molcel.2018.08.008
9 JS Gootenberg, OO Abudayyeh, MJ Kellner, J Joung, JJ Collins, F Zhang (2018) Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. Science 360:439–444
https://doi.org/10.1126/science.aaq0179
10 CA Freije, C Myhrvold, CK Boehm, AE Lin, NL Welch, A Carter, HC Metsky, CY Luo, OO Abudayyeh, JS Gootenberget al. (2019) Programmable inhibition and detection of RNA viruses using Cas13. Mol Cell 76:826–837.e811
https://doi.org/10.1016/j.molcel.2019.09.013
11 JS Gootenberg, OO Abudayyeh, JW Lee, P Essletzbichler, AJ Dy, J Joung, V Verdine, N Donghia, NM Daringer, CA Freijeet al. (2017) Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 356:438–442
https://doi.org/10.1126/science.aam9321
12 LB Harrington, D Burstein, JS Chen, D Paez-Espino, E Ma, IP Witte, JC Cofsky, NC Kyrpides, JF Banfield, JA Doudna (2018) Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. Science 362:839–842
https://doi.org/10.1126/science.aav4294
13 P Horvath, R Barrangou (2010) CRISPR/Cas, the immune system of bacteria and archaea. Science 327:167–170
https://doi.org/10.1126/science.1179555
14 M Huang, X Zhou, H Wang, D Xing (2018) Clustered regularly interspaced short palindromic repeats/Cas9 triggered isothermal amplification for site-specific nucleic acid detection. Anal Chem 90:2193–2200
https://doi.org/10.1021/acs.analchem.7b04542
15 Y Ishino, H Shinagawa, K, Makino M Amemura, A Nakata (1987) Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol 169:5429–5433
https://doi.org/10.1128/JB.169.12.5429-5433.1987
16 R Jansen, JD Embden, W Gaastra, LM Schouls (2002) Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol 43:1565–1575
https://doi.org/10.1046/j.1365-2958.2002.02839.x
17 S Jenkins, JC Yang, SS Ramalingam, K Yu, S Patel, S Weston, R Hodge, M Cantarini, PA Janne, T Mitsudomi (2017) Plasma ctDNA analysis for detection of the EGFR T790M mutation in patients with advanced non-small cell lung cancer. J Thorac Oncol 12:1061–1070
https://doi.org/10.1016/j.jtho.2017.04.003
18 C Jia, C Huai, J, Ding L Hu, B Su, H Chen, D Lu (2018) New applications of CRISPR/Cas9 system on mutant DNA detection. Gene 641:55–62
https://doi.org/10.1016/j.gene.2017.10.023
19 M Jinek, K Chylinski, I Fonfara, M Hauer, JA Doudna, E Charpentier (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–821
https://doi.org/10.1126/science.1225829
20 YGCM Kebed (2015) Review article: genetically modified crops and food security. Food Sci Qual Manage 42:41–49
21 S Konermann, P Lotfy, NJ Brideau, J Oki, MN Shokhirev, PD Hsu (2018) Transcriptome engineering with RNA-targeting type VI-D CRISPR effectors. Cell 173:665–676.e614
https://doi.org/10.1016/j.cell.2018.02.033
22 S-Y Li, Q-X Cheng, J-M Wang, X-Y Li, Z-L Zhang, S, Gao R-B Cao, G-P Zhao, J Wang(2018) CRISPR-Cas12a-assisted nucleic acid detection. Cell Discov 4:20
https://doi.org/10.1038/s41421-018-0028-z
23 L Li, S Li, N Wu, J Wu, G, Wang G, Zhao J Wang (2019) HOLMESv2: a CRISPR-Cas12b-assisted platform for nucleic acid detection and DNA methylation quantitation. ACS Synth Biol 8:2228–2237
https://doi.org/10.1021/acssynbio.9b00209
24 M, Liang Z, Li W Wang, J Liu, L Liu, G Zhu, L Karthik, M Wang, K-F, Wang Z Wang et al (2019) A CRISPR-Cas12a-derived biosensing platform for the highly sensitive detection of diverse small molecules. Nat Commun 10:3672
https://doi.org/10.1038/s41467-019-11648-1
25 HC Metsky, CA Freije, T-SF Kosoko-Thoroddsen, PC Sabeti, C Myhrvold (2020) CRISPR-based COVID-19 surveillance using a genomically-comprehensive machine learning approach. bioRxiv.
https://doi.org/10.1101/2020.02.26.967026
26 C Myhrvold, CA Freije, JS Gootenberg, OO Abudayyeh, HC Metsky, AF Durbin, MJ Kellner, AL Tan, LM Paul, LA Parhamet al. (2018) Field-deployable viral diagnostics using CRISPR-Cas13. Science 360:444–448
https://doi.org/10.1126/science.aas8836
27 K Pardee, AA Green, MK Takahashi, D Braff, G Lambert, JW Lee, T Ferrante, D Ma, N Donghia, M Fanet al. (2016) Rapid, low-cost detection of Zika virus using programmable biomolecular components. Cell 165:1255–1266
https://doi.org/10.1016/j.cell.2016.04.059
28 S Shmakov, O Abudayyeh Omar , S Makarova Kira, I Wolf Yuri, S Gootenberg Jonathan, E Semenova, L Minakhin, J Joung, S Konermann, K Severinov et al (2015) Discovery and functional characterization of diverse class 2 CRISPR-Cas systems. Mol Cell 60:385–397
https://doi.org/10.1016/j.molcel.2015.10.008
29 R Sorek, CM Lawrence, B Wiedenheft (2013) CRISPR-mediated adaptive immune systems in bacteria and archaea. Annu Rev Biochem 82:237–266
https://doi.org/10.1146/annurev-biochem-072911-172315
30 J Strecker, S Jones, B Koopal, J Schmid-Burgk , B Zetsche, L Gao, KS Makarova, EV Koonin, F Zhang (2019) Engineering of CRISPR-Cas12b for human genome editing. Nat Commun 10:212
https://doi.org/10.1038/s41467-018-08224-4
31 F Teng, T Cui, G Feng, L Guo, K Xu, Q Gao, T Li, J Li, Q Zhou, W Li (2018) Repurposing CRISPR-Cas12b for mammalian genome engineering. Cell Discov 4:63
https://doi.org/10.1038/s41421-018-0069-3
32 F Teng, T, Cui Q Gao, L Guo, H Wan, W Li (2019) Artificial sgRNAs engineered for genome editing with new Cas12b orthologs. Cell Discov 5:23
https://doi.org/10.1038/s41421-019-0091-0
33 X-W Wang, L-F Hu, J Hao, L-Q Liao, Y-T Chiu, M Shi, Y Wang (2019) A microRNA-inducible CRISPR–Cas9 platform serves as a microRNA sensor and cell-type-specific genome regulation tool. Nat Cell Biol 21:522–530
https://doi.org/10.1038/s41556-019-0292-7
34 WX Yan, S, Chong H Zhang, KS Makarova, EV Koonin, DR Cheng, DA Scott (2018) Cas13d is a compact RNA-targeting type VI CRISPR effector positively modulated by a WYL-domain-containing accessory protein. Mol Cell 70:327–339.e325
https://doi.org/10.1016/j.molcel.2018.02.028
35 WX Yan, P Hunnewell, LE Alfonse, JM Carte, E Keston-Smith , S Sothiselvam, AJ Garrity, S Chong, KS Makarova, EV Kooninet al. (2019) Functionally diverse type V CRISPR-Cas systems. Science 363:88
https://doi.org/10.1126/science.aav7271
36 B Zetsche, S Gootenberg Jonathan, O Abudayyeh Omar , M Slaymaker Ian, S Makarova Kira, P Essletzbichler, E, Volz Sara J Joung, J van der Oost, A Regevet al. (2015) Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163:759–771
https://doi.org/10.1016/j.cell.2015.09.038
37 K Zhang, R Deng, X Teng, Y Li, Y, Sun X Ren, J Li (2018) Direct visualization of single-nucleotide variation in mtDNA using a CRISPR/Cas9-mediated proximity ligation assay. J Am Chem Soc 140:11293–11301
https://doi.org/10.1021/jacs.8b05309
38 W Zhou, L Hu, L Ying, Z Zhao, PK Chu, X-F Yu (2018) A CRISPR–Cas9-triggered strand displacement amplification method for ultrasensitive DNA detection. Nat Commun 9:5012
https://doi.org/10.1038/s41467-018-07324-5
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