COMMENTARY

The expanded development and application of CRISPR system for sensitive nucleotide detection

  • Fengjing Jia 1 ,
  • Xuewen Li 4 ,
  • Chao Zhang , 1 ,
  • Xueming Tang , 2,3
Expand
  • 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

Published date: 15 Sep 2020

Copyright

2020 The Author(s)

Cite this article

Fengjing Jia , Xuewen Li , Chao Zhang , Xueming Tang . The expanded development and application of CRISPR system for sensitive nucleotide detection[J]. Protein & Cell, 2020 , 11(9) : 624 -629 . DOI: 10.1007/s13238-020-00708-8

1
Abudayyeh OO, Gootenberg JS, Konermann S, Joung J, Slaymaker IM, Cox DB, Shmakov S, Makarova KS, Semenova E, Minakhin L (2016) C2c2 is a single-component programmable RNAguided RNA-targeting CRISPR effector. Science 353:aaf5573

DOI

2
Abudayyeh OO, Gootenberg JS, Kellner MJ, Zhang F (2019) Nucleic acid detection of plant genes using CRISPR-Cas13. CRISPR J 2:165–171

DOI

3
Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW, Levy JM, Chen PJ, Wilson C, Newby GA, Raguram A (2019) Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576:149–157

DOI

4
Barrangou R, Marraffini Luciano A (2014) CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity. Mol Cell 54:234–244

DOI

5
Chang W, Liu W, Liu Y, Zhan F, Chen H, Lei H,Liu Y (2019) Colorimetric detection of nucleic acid sequences in plant pathogens based on CRISPR/Cas9 triggered signal amplification. Microchim Acta 186:243

DOI

6
Chen JS, Ma E, Harrington LB, Da Costa M, Tian X, Palefsky JM, Doudna JA (2018) CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science 360:436–439

DOI

7
East-Seletsky A, O’Connell MR, Knight SC, Burstein D, Cate JH, Tjian R, Doudna JA (2016) Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature 538:270–273

DOI

8
Field AE, Robertson N, Wang T, Havas A, Ideker T, Adams PD (2018) DNA methylation clocks in aging: categories, causes, and consequences. Mol Cell 71:882–895

DOI

9
Gootenberg JS, Abudayyeh OO, Kellner MJ, Joung J, Collins JJ, Zhang F (2018) Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. Science 360:439–444

DOI

10
Freije CA, Myhrvold C, Boehm CK, Lin AE, Welch NL, Carter A, Metsky HC, Luo CY, Abudayyeh OO, Gootenberg JS (2019) Programmable inhibition and detection of RNA viruses using Cas13. Mol Cell 76:826–837.e811

DOI

11
Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, Verdine V, Donghia N, Daringer NM, Freije CA (2017) Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 356:438–442

DOI

12
Harrington LB, Burstein D, Chen JS, Paez-Espino D, Ma E, Witte IP, Cofsky JC, Kyrpides NC, Banfield JF, Doudna JA (2018) Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. Science 362:839–842

DOI

13
Horvath P, Barrangou R (2010) CRISPR/Cas, the immune system of bacteria and archaea. Science 327:167–170

DOI

14
Huang M, Zhou X, Wang H, Xing D (2018) Clustered regularly interspaced short palindromic repeats/Cas9 triggered isothermal amplification for site-specific nucleic acid detection. Anal Chem 90:2193–2200

DOI

15
Ishino Y, Shinagawa H, Makino K,Amemura M, Nakata A (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

DOI

16
Jansen R, Embden JD, Gaastra W, Schouls LM (2002) Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol 43:1565–1575

DOI

17
Jenkins S, Yang JC, Ramalingam SS, Yu K, Patel S, Weston S, Hodge R, Cantarini M, Janne PA, Mitsudomi T (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

DOI

18
Jia C, Huai C, Ding J,Hu L, Su B, Chen H, Lu D (2018) New applications of CRISPR/Cas9 system on mutant DNA detection. Gene 641:55–62

DOI

19
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 337:816–821

DOI

20
Kebed YGCM (2015) Review article: genetically modified crops and food security. Food Sci Qual Manage 42:41–49

21
Konermann S, Lotfy P, Brideau NJ, Oki J, Shokhirev MN, Hsu PD (2018) Transcriptome engineering with RNA-targeting type VI-D CRISPR effectors. Cell 173:665–676.e614

DOI

22
Li S-Y, Cheng Q-X, Wang J-M, Li X-Y, Zhang Z-L, Gao S,Cao R-B, Zhao G-P, Wang J(2018) CRISPR-Cas12a-assisted nucleic acid detection. Cell Discov 4:20

DOI

23
Li L, Li S, Wu N, Wu J, Wang G,Zhao G,Wang J (2019) HOLMESv2: a CRISPR-Cas12b-assisted platform for nucleic acid detection and DNA methylation quantitation. ACS Synth Biol 8:2228–2237

DOI

24
Liang M,Li Z, Wang W, Liu J, Liu L, Zhu G, Karthik L,Wang M, Wang K-F,Wang Z et al (2019) A CRISPR-Cas12a-derived biosensing platform for the highly sensitive detection of diverse small molecules. Nat Commun 10:3672

DOI

25
Metsky HC, Freije CA, Kosoko-Thoroddsen T-SF, Sabeti PC, Myhrvold C (2020) CRISPR-based COVID-19 surveillance using a genomically-comprehensive machine learning approach. bioRxiv.https://doi.org/10.1101/2020.02.26.967026

DOI

26
Myhrvold C, Freije CA, Gootenberg JS, Abudayyeh OO, Metsky HC, Durbin AF, Kellner MJ, Tan AL, Paul LM, Parham LA (2018) Field-deployable viral diagnostics using CRISPR-Cas13. Science 360:444–448

DOI

27
Pardee K, Green AA, Takahashi MK, Braff D, Lambert G, Lee JW, Ferrante T, Ma D, Donghia N, Fan M (2016) Rapid, low-cost detection of Zika virus using programmable biomolecular components. Cell 165:1255–1266

DOI

28
Shmakov S, Abudayyeh Omar O, Makarova Kira S, Wolf Yuri I, Gootenberg Jonathan S, Semenova E, Minakhin L, Joung J, Konermann S, Severinov K et al (2015) Discovery and functional characterization of diverse class 2 CRISPR-Cas systems. Mol Cell 60:385–397

DOI

29
Sorek R, Lawrence CM, Wiedenheft B (2013) CRISPR-mediated adaptive immune systems in bacteria and archaea. Annu Rev Biochem 82:237–266

DOI

30
Strecker J, Jones S, Koopal B, Schmid-Burgk J, Zetsche B, Gao L, Makarova KS, Koonin EV, Zhang F (2019) Engineering of CRISPR-Cas12b for human genome editing. Nat Commun 10:212

DOI

31
Teng F, Cui T, Feng G, Guo L, Xu K, Gao Q, Li T, Li J, Zhou Q, Li W (2018) Repurposing CRISPR-Cas12b for mammalian genome engineering. Cell Discov 4:63

DOI

32
Teng F, Cui T, Gao Q, Guo L, Wan H, Li W (2019) Artificial sgRNAs engineered for genome editing with new Cas12b orthologs. Cell Discov 5:23

DOI

33
Wang X-W, Hu L-F, Hao J, Liao L-Q, Chiu Y-T, Shi M, Wang Y (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

DOI

34
Yan WX, Chong S, Zhang H, Makarova KS, Koonin EV, Cheng DR, Scott DA (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

DOI

35
Yan WX, Hunnewell P, Alfonse LE, Carte JM, Keston-Smith E, Sothiselvam S, Garrity AJ, Chong S, Makarova KS, Koonin EV (2019) Functionally diverse type V CRISPR-Cas systems. Science 363:88

DOI

36
Zetsche B, Gootenberg Jonathan S, Abudayyeh Omar O, Slaymaker Ian M, Makarova Kira S, Essletzbichler P, Volz Sara E,Joung J, van der Oost J, Regev A (2015) Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163:759–771

DOI

37
Zhang K, Deng R, Teng X, Li Y, Sun Y,Ren X, Li J (2018) Direct visualization of single-nucleotide variation in mtDNA using a CRISPR/Cas9-mediated proximity ligation assay. J Am Chem Soc 140:11293–11301

DOI

38
Zhou W, Hu L, Ying L, Zhao Z, Chu PK, Yu X-F (2018) A CRISPR–Cas9-triggered strand displacement amplification method for ultrasensitive DNA detection. Nat Commun 9:5012

DOI

Outlines

/