摘要由规律成簇间隔短回文重复序列(clustered regularly interspaced short palindromic repeats,CRISPR)以及CRISPR相关蛋白9(CRISPR-associated protein 9, Cas9)组成的系统被发现广泛存在于细菌及古菌中,是机体长期进化形成的由RNA指导的降解外源遗传物质的适应性免疫系统。由于该系统可以识别靶向序列完成DNA的双链切割,因此从2013年起,CRISPR/Cas9系统即被改造为基因编辑工具。作为一种新型的基因组编辑技术,CRISPR/Cas9系统具有设计简单、特异性强、效率高等优点,为基因组定向改造调控和应用带来了突破性的革命,并且迅速在基础理论、转基因动物生产、基因诊断和临床治疗等领域中得到广泛的研究与应用。然而,CRISPR/Cas9也存在着脱靶效应和外源基因插入困难等一些亟待解决的问题,这在一定程度上限制了CRISPR/Cas9 的应用。因此,近年来围绕CRISPR系统改进获得了一系列可用于基因编辑与基因表达修饰的新工具。本文介绍了CRISPR系统的组成、工作原理,并综述了近几年来基于CRISPR系统开发的几种新型基因编辑工具以及基因表达修饰工具的研究进展和应用,并对其应用前景和发展方向进行了展望。
Abstract:Bacteria and archaea have evolved an adaptive immune system, which was known as clustered regularly interspaced short palindromic repeats (CRISPR) / CRISPR -associated protein (Cas 9) system, and that uses short RNA to degrade the target sequences present in invading viral and phage DNAs. This system can identify the target sequence and cut the double-stranded DNA. So, it has been harnessed by thousands of laboratories for genome editing applications in a variety of experimental model systems since 2013. As a new type of genome editing techniques, the CRISPR/Cas9 system has advantages in simple in design, strong specificity and high efficiency. CRISPR/Cas9 system has brought a breakthrough in genome directional regulation and application, and rapidly applied in the basic theory, transgenic animal production, genetic diagnosis, clinical therapy fields. Whereas, every new technology has its limitations, CRISPR/Cas9 system also exists off-target effects and difficulty to insert genes. This limits its applications to some extent. Therefore, around the CRISPR system, many scientists improved a series of modification that can be used for the gene editing and gene expression of new tools in recent years. Here, we reviewed the research progress and application of new gene editing tools and gene expression modification based on the CRISPR system evolution and looking forward to the application prospect and development direction.
1. Bibikova M, Golic M, Golic KG. Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases. Genetics, 2002, 161(3): 1169–1175. 2. Dreier B, Fuller RP, Segal DJ. Development of zinc finger domains for recognition of the 5’-CNN-3’ family DNA sequences and their use in the construction of artificial transcription factors. J Biol Chem, 2005, 280(42): 35588–35597. 3. Bibikova M, Beumer K, Trautman JK. Enhancing gene targeting with designed zinc finger nucleases. Science, 2003, 300(5620): 764. 4. Shan QW, Wang YP, Chen KL. Rapid and efficient gene modification in rice and Brachypodium using TALENs. Mol Plant, 2013, 6(4): 1365–1368. 5. Hockemeyer D, Wang HY, Kiani S. Genetic engineering of human pluripotent cells using TALE nucleases. Nat Biotechnol, 2011, 29(8): 731–734. 6. Huang P, Xiao A, Zhou MG. Heritable gene targeting in zebrafish using customized TALENs. Nat Biotechnol, 2011, 29(8): 699-700. 7. Tesson L, Usal C, Ménoret S. Knockout rats generated by embryo microinjection of TALENs. Nat Biotechnol, 2011, 29(8): 695–696. 8.Shan QW, Wang YP, Li J. Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol, 2013, 31(8): 686–688. 9.Li JF, Norville JE, Aach J. Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat Biotechnol, 2013, 31(8): 688–691.10.Cong L, Ran FA, Cox D. Multiplex genome engineering using CRISPR/Cas systems. Science, 2013, 339(6121): 819-823. 11.Hwang WY, Fu YF, Reyon D. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol, 2013, 31(3): 227–229. 12. Jiang WY, Bikard D, Cox D. RNA-guided editing of bacterial genomes using CRISPR- Cas systems. Nat Biotechnol, 2013, 31(3): 233–239. 13.DiCarlo JE, Norville JE, Mali P. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res, 2013, 41(7): 4336–4343.14.Ishino Y, Shinagawa H, Makino K. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol. 1987, 169(12):5429-33.15.Gasiunas G, Siksnys V. RNA-dependent DNA endonuclease Cas9 of the CRISPR system: Holy Grail of genome editing? Trends Microbiol. 2013, 21(11):562-7. 16.Jinek M, Chylinski K, Fonfara I. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012. 337(6096):816-21.17. Zetsche B, Gootenberg JS, Abudayyeh OO. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell. 2015, 163(3):759-71.18. Fonfara I, Richter H, Bratovi? M. The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA. Nature. 2016, 532(7600):517-21.19. Zetsche B, Heidenreich M, Mohanraju P. Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array. Nat Biotechnol. 2017, 35(1):31-34.20. Kim H, Kim ST, Ryu J. CRISPR/Cpf1-mediated DNA-free plant genome editing. Nat Commun. 2017, 8:14406.21. Nishida K, Arazoe T, Yachie N.Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems.Science. 2016, 353(6305). 22. Ma Y, Zhang J, Yin W. Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells.Nat Methods. 2016 , 13(12):1029-1035.23. Kuscu C, Parlak M, Tufan T. CRISPR-STOP: gene silencing through base-editing-induced nonsense mutations. Nat Methods. 2017, 14(7): 710-712. 24.Ma H, Tu LC, Naseri A. Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow.Nat Biotechnol. 2016, 34(5):528-30. 25. Anderson DM, Anderson KM, Chang CL. A micropeptide encoded by a putative long noncoding RNA regulates muscle performance. Cell. 2015, 160(4):595-606.26. Nelles DA, Fang MY, O'Connell MR. Programmable RNA Tracking in Live Cells with CRISPR/Cas9. Cell. 2016, 165(2):488-96.27. Abudayyeh OO, Gootenberg JS, Konermann S. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science. 2016, 353(6299):aaf5573.28. East-Seletsky A, O'Connell MR, Knight SC. Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature. 2016, 538(7624):270-273.29. Gootenberg JS, Abudayyeh OO, Lee JW. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science. 2017, 356(6336):438-442.30. Perez-Pinera P, Kocak DD, Vockley CM. RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat Methods. 2013, 10(10):973-6. 31. Balboa D, Weltner J, Eurola S. Conditionally Stabilized dCas9 Activator for Controlling Gene Expression in Human Cell Reprogramming and Differentiation.Stem Cell Reports. 2015, 5(3):448-59. 32. Maeder ML, Linder SJ, Cascio VM. CRISPR RNA-guided activation of endogenous human genes.Nat Methods. 2013, 10(10):977-9.33. Xiong K, Zhou Y, Blichfeld KA. RNA-Guided Activation of Pluripotency Genes in Human Fibroblasts.Cell Reprogram. 2017, 19(3):189-198. 34. Gilbert LA, Horlbeck MA, Adamson B.Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.Cell. 2014, 159(3):647-61. 35. Qi LS, Larson MH, Gilbert LA.Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression.Cell. 2013,152(5):1173-83.36. Gilbert LA, Larson MH, Morsut L. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes.Cell. 2013 Jul 18;154(2):442-51.37. Li D, Lv L, Chen JC. Controlling microbial PHB synthesis via CRISPRi. Appl Microbiol Biotechnol. 2017 Jun 15. 38. Wang Y, Zhang ZT, Seo SO. Gene transcription repression in Clostridium beijerinckii using CRISPR-dCas9.Biotechnol Bioeng. 2016 Dec;113(12):2739-2743.39. Rosenbluh J, Xu H, Harrington W. Complementary information derived from CRISPR Cas9 mediated gene deletion and suppression.Nat Commun. 2017, 8:15403.40. Zhang X, Wang J, Cheng Q. Multiplex gene regulation by CRISPR-ddCpf1. Cell Discov. 2017, 3:17018. 41. Ho TT, Zhou N, Huang J. Targeting non-coding RNAs with the CRISPR/Cas9 system in human cell lines.Nucleic Acids Res. 2015, ;43(3):e17.42. Zhen S, Hua L, Liu YH. Inhibition of long non-coding RNA UCA1 by CRISPR/Cas9 attenuated malignant phenotypes of bladder cancer.Oncotarget. 2017 , 8(6):9634-9646.43. Liu SJ, Horlbeck MA, Cho SW. CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells.Science. 2017, 355(6320). 44. Ma T, Tao J, Yang M, et al. An AANAT/ASMT transgenic animal model constructed with CRISPR/Cas9 system serving as the mammary gland bioreactor to produce melatonin‐enriched milk in sheep[J]. Journal of Pineal Research, 2017.45. Schaefer KA, Wu WH, Colgan DF.Unexpected mutations after CRISPR-Cas9 editing in vivo.Nat Methods. 2017, 14(6):547-548.