RNA靶向系统CRISPR/Cas13的研究进展及应用
刘园 （ 广州医科大学附属第六医院 广州医科大学基础医学院，中法霍夫曼免疫研究所； 呼吸疾病国家重点实验室 深圳市罗湖区人民医院，深圳大学附属第三医院 ）
谢庆强 （ 广州医科大学附属第六医院 广州医科大学基础医学院，中法霍夫曼免疫研究所； 呼吸疾病国家重点实验室 ）
李雪峰 （ 广州医科大学附属第六医院 广州医科大学基础医学院，中法霍夫曼免疫研究所； 呼吸疾病国家重点实验室 深圳市罗湖区人民医院，深圳大学附属第三医院 ）
https://doi.org/10.37155/2717-5693-0102-3Abstract
成簇的规则间隔的短回文重复序列（Clustered Regularly Interspaced Short Palindromic Repeats，CRISPR）和CRISPR相关蛋白（CRISPR-associated，Cas）系统是大多数细菌体内抵抗噬菌体入侵的获得性免疫系统，经改造后，被开发成一种高效的基因编辑工具。不同于DNA靶向的CRISPR相关酶（如Cas9和Cpf1），靶向RNA的CRISPR相关酶Cas13被发现是一种具有“附带切割”活性的新型核酸酶，其在切割靶标RNA后继续切割其他的非靶标RNA。此外，突变导致的无核酸酶活性的Cas13（dCas13）能够结合目标RNA但无法切割。基于Cas13的这些特性，Cas13蛋白已被应用于多种类型的RNA研究，如RNA定点编辑、RNA敲低、RNA检测和RNA成像。本文主要对CRISPR/Cas13系统在近几年的研究进展和应用进行综述。
Keywords
CRISPR/Cas13; 附带切割; 核酸酶; RNA研究Full Text
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31. Rao DD, Vorhies JS, Senzer N, Nemunaitis J: siRNA vs. shRNA: similarities and differences. Adv Drug Deliv Rev 2009, 61(9):746-759.
32. Boettcher M, McManus MT: Choosing the Right Tool for the Job: RNAi, TALEN, or CRISPR. Molecular cell 2015, 58(4):575-585.
33. Abudayyeh OO, Gootenberg JS, Essletzbichler P, Han S, Joung J, Belanto JJ, Verdine V, Cox DBT, Kellner MJ, Regev A et al: RNA targeting with CRISPR-Cas13. Nature 2017, 550(7675):280-284.
34. Wilson RC, Doudna JA: Molecular mechanisms of RNA interference. Annu Rev Biophys 2013, 42:217-239.
35. Unniyampurath U, Pilankatta R, Krishnan MN: RNA Interference in the Age of CRISPR: Will CRISPR Interfere with RNAi? Int J Mol Sci 2016, 17(3):291-291.
36. Granados-Riveron JT, Aquino-Jarquin G: CRISPR-Cas13 Precision Transcriptome Engineering in Cancer. Cancer research 2018, 78(15):4107-4113.
37. Aman R, Ali Z, Butt H, Mahas A, Aljedaani F, Khan MZ, Ding S, Mahfouz M: RNA virus interference via CRISPR/Cas13a system in plants. Genome Biol 2018, 19(1):1-1.
38. Aman R, Mahas A, Butt H, Aljedaani FA-OX, Mahfouz M: Engineering RNA Virus Interference via the CRISPR/Cas13 Machinery in Arabidopsis. LID - 10.3390/v10120732 [doi] LID - 732. Viruses 2018 Dec 19, 10(12):732.
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41. He B, Peng W, Huang J, Zhang H, Zhou Y, Yang X, Liu J, Li Z, Xu C, Xue M et al: Modulation of metabolic functions through Cas13d-mediated gene knockdown in liver. Protein Cell 2020 Mar 18:1-7.
42. Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, Verdine V, Donghia N, Daringer NM, Freije CA et al: Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 2017, 356(6336):438-442.
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47. Shan Y, Zhou X, Huang R, Xing D: High-Fidelity and Rapid Quantification of miRNA Combining crRNA Programmability and CRISPR/Cas13a trans-Cleavage Activity. Anal Chem 2019, 91(8):5278-5285.
48. Chen Y, Yang S, Peng S, Li W, Wu F, Yao Q, Wang F, Weng X, Zhou X: N1-Methyladenosine detection with CRISPR-Cas13a/C2c2. Chem Sci 2019, 10(10):2975-2979.
49. Shen J, Zhou X, Shan Y, Yue H, Huang R, Hu JA-Ohoo, Xing D: Sensitive detection of a bacterial pathogen using allosteric probe-initiated catalysis and CRISPR-Cas13a amplification reaction. Nat Commun 2020 Jan 14, 11(1):267.
50. Bruch R, Baaske J, Chatelle C, Meirich M, Madlener S, Weber W, Dincer C, Urban GA: CRISPR/Cas13a-Powered Electrochemical Microfluidic Biosensor for Nucleic Acid Amplification-Free miRNA Diagnostics. Advanced materials (Deerfield Beach, Fla) 2019, 31(51):e1905311-e1905311.
51. Chen Q, Tian T, Xiong E, Wang P, Zhou X: CRISPR/Cas13a Signal Amplification Linked Immunosorbent Assay for Femtomolar Protein Detection. Anal Chem 2020, 92(1):573-577.
52. Yuan C, Tian T, Sun J, Hu M, Wang X, Xiong E, Cheng M, Bao Y, Lin W, Jiang J et al: Universal and Naked-Eye Gene Detection Platform Based on CRISPR/Cas12a/13a System. Anal Chem 2020:10.1021/acs.analchem.1029b05597.
53. Konermann S, Lotfy P, Brideau NJ, Oki J, Shokhirev MN, Hsu PD: Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors. Cell 2018 Apr 19, 173(3):665-676.e614. .
54. Yang LZ, Wang Y, Li SQ, Yao RW, Luan PF, Wu H, Carmichael GG, Chen LL: Dynamic Imaging of RNA in Living Cells by CRISPR-Cas13 Systems. Mol Cell 2019 Dec 19, 76(6):981-997.e987.
55. Rauch S, He E, Srienc M, Zhou H, Zhang Z, Dickinson BC: Programmable RNA-Guided RNA Effector Proteins Built from Human Parts. Cell 2019, 178(1):122-134.e112.
2. Koonin EV, Makarova KS, Zhang F: Diversity, classification and evolution of CRISPR-Cas systems. Curr Opin Microbiol 2017, 37:67-78.
3. Mohanraju P, Makarova KS, Zetsche B, Zhang F, Koonin EV, van der Oost J: Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems. Science 2016, 353(6299):aad5147
4. Makarova KS, Haft Dh Fau - Barrangou R, Barrangou R Fau - Brouns SJJ, Brouns Sj Fau - Charpentier E, Charpentier E Fau - Horvath P, Horvath P Fau - Moineau S, Moineau S Fau - Mojica FJM, Mojica Fj Fau - Wolf YI, Wolf Yi Fau - Yakunin AF, Yakunin Af Fau - van der Oost J et al: Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol 2011, 9(6):467-477.
5. Makarova KS, Zhang F, Koonin EV: SnapShot: Class 1 CRISPR-Cas Systems. Cell 2017, 168(5):946-946.e941.
6. Makarova KS, Zhang F, Koonin EV: SnapShot: Class 2 CRISPR-Cas Systems. Cell 2017, 168(1-2):328-328.e321.
7. Jacinto FV, Link W, Ferreira BI: CRISPR/Cas9-mediated genome editing: From basic research to translational medicine. J Cell Mol Med 2020:10.1111/jcmm.14916.
8. Abudayyeh OO, Gootenberg JS, Konermann S, Joung J, Slaymaker IM, Cox DBT, Shmakov S, Makarova KS, Semenova E, Minakhin L et al: C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science 2016, 353(6299):aaf5573-aaf5573.
9. Shmakov S, Abudayyeh OO, Makarova KS, Wolf YI, Gootenberg JS, Semenova E, Minakhin L, Joung J, Konermann S, Severinov K et al: Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems. Molecular cell 2015, 60(3):385-397.
10. East-Seletsky A, O'Connell MR, Knight SC, Burstein D, Cate JHD, Tjian R, Doudna JA: Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature 2016, 538(7624):270-273.
11. Knott GJ, East-Seletsky A, Cofsky JC, Holton JM, Charles E, O'Connell MR, Doudna JA: Guide-bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme. Nat Struct Mol Biol 2017, 24(10):825-833.
12. East-Seletsky A, O'Connell MR, Burstein D, Knott GJ, Doudna JA: RNA Targeting by Functionally Orthogonal Type VI-A CRISPR-Cas Enzymes. Molecular cell 2017, 66(3):373-383.e373.
13. Liu L, Li X, Wang J, Wang M, Chen P, Yin M, Li J, Sheng G, Wang Y: Two Distant Catalytic Sites Are Responsible for C2c2 RNase Activities. Cell 2017 Jan 12, 168(1-2):121-134.e112.
14. Slaymaker IM, Mesa P, Kellner MJ, Kannan S, Brignole E, Koob J, Feliciano PR, Stella S, Abudayyeh OO, Gootenberg JS et al: High-Resolution Structure of Cas13b and Biochemical Characterization of RNA Targeting and Cleavage. Cell Rep 2019 Mar 26, 26(13):3741-3751.e3745. .
15. Zhang B, Ye W, Ye Y, Zhou H, Saeed A, Chen J, Lin J, Perčulija V, Chen Q, Chen CJ et al: Structural insights into Cas13b-guided CRISPR RNA maturation and recognition. Cell Res 2018 Dec, 28(12):1198-1201.
16. Zhang BA-O, Ye Y, Ye W, Perčulija V, Jiang H, Chen Y, Li Y, Chen J, Lin J, Wang S et al: Two HEPN domains dictate CRISPR RNA maturation and target cleavage in Cas13d. Nat Commun 2019 Jun 11, 10(1):2544.
17. Liu L, Li X, Ma J, Li Z, You L, Wang J, Wang M, Zhang X, Wang Y: The Molecular Architecture for RNA-Guided RNA Cleavage by Cas13a. Cell 2017, 170(4):714-726.e710.
18. Liu L, Li X, Wang J, Wang M, Chen P, Yin M, Li J, Sheng G, Wang Y: Two Distant Catalytic Sites Are Responsible for C2c2 RNase Activities. Cell 2017, 168(1-2):121-134.e112.
19. Hsu PD, Lander ES, Zhang F: Development and applications of CRISPR-Cas9 for genome engineering. Cell 2014, 157(6):1262-1278.
20. Komor AC, Badran AH, Liu DR: CRISPR-Based Technologies for the Manipulation of Eukaryotic Genomes. Cell 2017, 168(1-2):20-36.
21. Jing X, Xie B, Chen L, Zhang N, Jiang Y, Qin H, Wang H, Hao P, Yang S, Li X: Implementation of the CRISPR-Cas13a system in fission yeast and its repurposing for precise RNA editing. Nucleic Acids Res 2018 Sep 6, 46(15):e90.
22. Cox DA-O, Gootenberg JA-O, Abudayyeh OA-O, Franklin BA-O, Kellner MA-O, Joung J, Zhang FA-O: RNA editing with CRISPR-Cas13. Science 2017 Nov 24, 358(6366):1019-1027.
23. Cox DBT, Gootenberg JS, Abudayyeh OO, Franklin B, Kellner MJ, Joung J, Zhang F: RNA editing with CRISPR-Cas13. Science 2017, 358(6366):1019-1027.
24. Zhao X, Liu L, Lang J, Cheng K, Wang Y, Li X, Shi J, Wang Y, Nie G: A CRISPR-Cas13a system for efficient and specific therapeutic targeting of mutant KRAS for pancreatic cancer treatment. Cancer Lett 2018, 431:171-181.
25. Ding M, Zhan H, Liao X, Li A, Zhong Y, Gao Q, Liu Y, Huang W, Cai Z: Enhancer RNA - P2RY2e induced by estrogen promotes malignant behaviors of bladder cancer. Int J Biol Sci 2018 Jul 27, 14(10):1268-1276.
26. Qi F, Tan B, Ma F, Zhu B, Zhang L, Liu X, Li H, Yang J, Cheng B: A Synthetic Light-switchable System based on CRISPR Cas13a Regulates the Expression of LncRNA MALAT1 and Affects the Malignant Phenotype of Bladder Cancer Cells. Int J Biol Sci 2019, 15(8):1630-1636.
27. Fan J, Liu Y, Liu L, Huang Y, Li X, Huang W: A Multifunction Lipid-Based CRISPR-Cas13a Genetic Circuit Delivery System for Bladder Cancer Gene Therapy. ACS Synth Biol 2020:10.1021/acssynbio.1029b00349.
28. Wang Q, Liu X, Zhou J, Yang C, Wang G, Tan Y, Wu Y, Zhang S, Yi K, Kang C: The CRISPR-Cas13a Gene-Editing System Induces Collateral Cleavage of RNA in Glioma Cells. Adv Sci (Weinh) 2019, 6(20):1901299-1901299.
29. Zhang Z, Wang Q, Liu Q, Zheng Y, Zheng C, Yi K, Zhao Y, Gu Y, Wang Y, Wang C et al: Dual-Locking Nanoparticles Disrupt the PD-1/PD-L1 Pathway for Efficient Cancer Immunotherapy. Adv Mater 2019 Dec, 31(51):e1905751.
30. Jackson AL, Bartz SR, Schelter J, Kobayashi SV, Burchard J, Mao M, Li B, Cavet G, Linsley PS: Expression profiling reveals off-target gene regulation by RNAi. Nat Biotechnol 2003, 21(6):635-637.
31. Rao DD, Vorhies JS, Senzer N, Nemunaitis J: siRNA vs. shRNA: similarities and differences. Adv Drug Deliv Rev 2009, 61(9):746-759.
32. Boettcher M, McManus MT: Choosing the Right Tool for the Job: RNAi, TALEN, or CRISPR. Molecular cell 2015, 58(4):575-585.
33. Abudayyeh OO, Gootenberg JS, Essletzbichler P, Han S, Joung J, Belanto JJ, Verdine V, Cox DBT, Kellner MJ, Regev A et al: RNA targeting with CRISPR-Cas13. Nature 2017, 550(7675):280-284.
34. Wilson RC, Doudna JA: Molecular mechanisms of RNA interference. Annu Rev Biophys 2013, 42:217-239.
35. Unniyampurath U, Pilankatta R, Krishnan MN: RNA Interference in the Age of CRISPR: Will CRISPR Interfere with RNAi? Int J Mol Sci 2016, 17(3):291-291.
36. Granados-Riveron JT, Aquino-Jarquin G: CRISPR-Cas13 Precision Transcriptome Engineering in Cancer. Cancer research 2018, 78(15):4107-4113.
37. Aman R, Ali Z, Butt H, Mahas A, Aljedaani F, Khan MZ, Ding S, Mahfouz M: RNA virus interference via CRISPR/Cas13a system in plants. Genome Biol 2018, 19(1):1-1.
38. Aman R, Mahas A, Butt H, Aljedaani FA-OX, Mahfouz M: Engineering RNA Virus Interference via the CRISPR/Cas13 Machinery in Arabidopsis. LID - 10.3390/v10120732 [doi] LID - 732. Viruses 2018 Dec 19, 10(12):732.
39. Zhan X, Zhang F, Zhong Z, Chen R, Wang Y, Chang L, Bock RA-O, Nie B, Zhang JA-O: Generation of virus-resistant potato plants by RNA genome targeting. Plant Biotechnol J 2019 Sep, 17(9):1814-1822.
40. Konermann S, Lotfy P, Brideau NJ, Oki J, Shokhirev MN, Hsu PD: Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors. Cell 2018 Apr 19, 173(3):665-676.e614.
41. He B, Peng W, Huang J, Zhang H, Zhou Y, Yang X, Liu J, Li Z, Xu C, Xue M et al: Modulation of metabolic functions through Cas13d-mediated gene knockdown in liver. Protein Cell 2020 Mar 18:1-7.
42. Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, Verdine V, Donghia N, Daringer NM, Freije CA et al: Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 2017, 356(6336):438-442.
43. Gootenberg JA-O, Abudayyeh OA-O, Kellner MA-O, Joung J, Collins JJ, Zhang FA-O: Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. science 2018 Apr 27, 360(6387):439-444.
44. Chang Y, Deng Y, Li T, Wang J, Wang T, Tan F, Li X, Tian K: Visual detection of porcine reproductive and respiratory syndrome virus using CRISPR-Cas13a. Transbound Emerg Dis 2019:10.1111/tbed.13368.
45. Liu Y, Xu H, Liu C, Peng L, Khan H, Cui L, Huang R, Wu C, Shen S, Wang S et al: CRISPR-Cas13a Nanomachine Based Simple Technology for Avian Influenza A (H7N9) Virus On-Site Detection. J Biomed Nanotechnol 2019, 15(4):790-798.
46. Qin P, Park M, Alfson KJ, Tamhankar M, Carrion R, Patterson JL, Griffiths A, He Q, Yildiz A, Mathies R et al: Rapid and Fully Microfluidic Ebola Virus Detection with CRISPR-Cas13a. ACS Sens 2019, 4(4):1048-1054.
47. Shan Y, Zhou X, Huang R, Xing D: High-Fidelity and Rapid Quantification of miRNA Combining crRNA Programmability and CRISPR/Cas13a trans-Cleavage Activity. Anal Chem 2019, 91(8):5278-5285.
48. Chen Y, Yang S, Peng S, Li W, Wu F, Yao Q, Wang F, Weng X, Zhou X: N1-Methyladenosine detection with CRISPR-Cas13a/C2c2. Chem Sci 2019, 10(10):2975-2979.
49. Shen J, Zhou X, Shan Y, Yue H, Huang R, Hu JA-Ohoo, Xing D: Sensitive detection of a bacterial pathogen using allosteric probe-initiated catalysis and CRISPR-Cas13a amplification reaction. Nat Commun 2020 Jan 14, 11(1):267.
50. Bruch R, Baaske J, Chatelle C, Meirich M, Madlener S, Weber W, Dincer C, Urban GA: CRISPR/Cas13a-Powered Electrochemical Microfluidic Biosensor for Nucleic Acid Amplification-Free miRNA Diagnostics. Advanced materials (Deerfield Beach, Fla) 2019, 31(51):e1905311-e1905311.
51. Chen Q, Tian T, Xiong E, Wang P, Zhou X: CRISPR/Cas13a Signal Amplification Linked Immunosorbent Assay for Femtomolar Protein Detection. Anal Chem 2020, 92(1):573-577.
52. Yuan C, Tian T, Sun J, Hu M, Wang X, Xiong E, Cheng M, Bao Y, Lin W, Jiang J et al: Universal and Naked-Eye Gene Detection Platform Based on CRISPR/Cas12a/13a System. Anal Chem 2020:10.1021/acs.analchem.1029b05597.
53. Konermann S, Lotfy P, Brideau NJ, Oki J, Shokhirev MN, Hsu PD: Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors. Cell 2018 Apr 19, 173(3):665-676.e614. .
54. Yang LZ, Wang Y, Li SQ, Yao RW, Luan PF, Wu H, Carmichael GG, Chen LL: Dynamic Imaging of RNA in Living Cells by CRISPR-Cas13 Systems. Mol Cell 2019 Dec 19, 76(6):981-997.e987.
55. Rauch S, He E, Srienc M, Zhou H, Zhang Z, Dickinson BC: Programmable RNA-Guided RNA Effector Proteins Built from Human Parts. Cell 2019, 178(1):122-134.e112.
Copyright © 2020 刘园, 谢庆强, 李雪峰
Publishing time:2020-06-24
This work is licensed under a Creative Commons Attribution 4.0 International License
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