|
|
|
| Progress of Next-generation Targeted Gene-editing Techniques |
| YANG Fa-yu, GE Xiang-lian, GU Feng |
| School of Ophthalmology and Optometry, Wenzhou Medical University, State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou 325000, China |
|
|
|
Abstract Manipulating genomes by traditional targeted genome editing technique (gene targeting) is inefficient, making it impractical or difficult to use the technique as a gene-therapy approach to cure diseases and decipher gene functions. To overcome this problem, next-generation targeted gene-editing techniques were developed to achieve higher efficiency for gene correction, specific locus integration or knock-in and high throughput gene knock-out. The progress of new techniques for targeted genome-editing tools were reviewed, including zinc finger nucleases (ZFN), transcription activator-like effector nucleases (TALENs), and a clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system. A brief summary of the history, recent structure, progress, and future prospects was presented. After comparing these tools, it was found that CRISPR systems offer an advantage over ZFN and TALEN.
|
|
Received: 18 October 2013
Published: 25 February 2014
|
|
|
|
|
[1] Chamberlain J R, Schwarze U, Russell D W, et al. Gene targeting in stem cells from individuals with osteogenesis imperfecta. Science, 2004, 303(5661): 1198-1201.
[2] Johnson L, Mercer K, Jacks T, et al. Somatic activation of the K-ras oncogene causes early onset lung cancer in mice. Nature, 2001, 410(6832): 1111-1116.
[3] Beard C, Hochedlinger K, Jaenisch R, et al. Efficient method to generate single-copy transgenic mice by site-specific integration in embryonic stem cells. Genesis, 2006, 44(1): 23-28.
[4] Pentao Liu, Nancy A J, Neal G C. A highly efficient recombineering-based method for generating conditional knockout mutations. Genome Res, 2003, 13(3): 476-484.
[5] Ellis H M, Yu D, Court D L, et al. High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides. Proc Natl Acad Sci U S A, 2001,98(12):6742-6746.
[6] Miller D G, Wang P R, Russell D W, et al. Gene targeting in vivo by adeno-associated virus vectors. Nat Biotechnol, 2006, 24(8): 1022-1026
[7] Miller J, McLaehlan A D, Klug A, et al. Repetitive zinc binding domains in the protein transcription factor ⅢA from Xenopus oocytes. EMBO J, 1985, 4(6): 1609-1614.
[8] Kim Y G, Chandrasegaran S. Chimeric restriction endonuclease. PNAS, 1994, 91(3): 883-887.
[9] Christine Merlin, Lauren E Beaver, Orley R Taylor, et al. Efficient targeted mutagenesis in the monarch butterfly using zinc-finger nucleases. Genome Research, 2013, 23: 159-168.
[10] Boch J, Bonas U. Xanthomonas AvrBs3 family-type III effectors: discovery and function. Annu Rev Phytopathol, 2010, 48: 419-436.
[11] Bonas U, Stall R E, Staskawicz B, et al. Genetic and structural characterization of the avirulence gene avrBs3 from Xanthomonas campestris pv. vesicatoria. Mol Gen Genet,1989, 218(1): 127-136.
[12] Kay S, Hahn S, Marois E, et al. A bacterial effector acts as a plant transcription factor and induces a cell size regulator. Science, 2007, 318(5850): 648-651
[13] Moscou M J, Bogdanove A J. A simple cipher governs DNA recognition by TAL effectors. Science, 2009, 326(5959): 1501.
[14] Cong L, Zhou R H, Kuo Y C, et al. Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains. Nat Commun, 2012, 3(7): 968.
[15] Wang H, Hu Y C, Markoulaki S, et al. TALEN-mediated editing of the mouse Y chromosome. Nat Biotechnol, 2013, 31(6): 530-532.
[16] Lombardo A, Genovese P, Beausejour C M, et al. Gene editing in human stem cells using zinc finger nucleases and integrase-defective lentiviral vector delivery. Nat Biotechnol, 2007, 25(11): 1298-1306.
[17] Hockemeyer D, Wang H, Kiani S, et al. Genetic engineering of human pluripotent cells using TALE nucleases. Nat Biotechnol, 2011, 29(8): 731-734.
[18] Wang H, Hu Y C, Jaenisch R.TALEN-mediated editing of the mouse Y chromosome.Nat Biotechnol, 2013,31(6):530-532.
[19] Ishino Y, Shinagawa H, Makino K, et al. 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): 5429-5433.
[20] Mojica F J, Diez-Villasenor C, Soria E, et al. Biological significance of a family of regularly spaced repeats in the genomes of Archaea, bacteria and mitochondria. Mol Microbiol, 2000, 36(1): 244-246.
[21] Jansen R, Embden J D, Gaastra W, et al. Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol, 2002, 43 (6): 1565-1575.
[22] Grissa I, Vergnaud G, Pourcel C, et al. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics, 2007, 8: 172.
[23] Karginov F V, Hannon G J. The CRISPR system: small RNA-guided defense in bacteria and archaea. Mol Cell, 2010, 37(1): 7-19.
[24] Deveau H, Garneau J E, Moineau S, et al. CRISPR/Cas system and its role in phage-bacteria interactions. Ann Rev Microbiol, 2010, 64: 475-493.
[25] Marraffini L A, Sontheimer E J. CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat Rev Genet, 2010, 11(3): 181-190.
[26] Cong L, Ran F A, Cox D, et al. Multiplex genome engineering using CRISPR/Cas systems. Science, 2013, 339(6121): 819-823.
[27] Lei S Q, Matthew H Larson, Luke A, et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell, 2013, 152: 1173-1183.
[28] Ran F A, Hsu P D, Zhang F, et al. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell, 2013, 154(6): 1380-1389.
[29] Fu Y, Foden J A, Khayter C, et al. High-frequency off-target mutagenesis induced by CRISPR -Cas nucleases in human cells. Nat Biotechnol, 2013, 31(9): 822-826.
[30] Rudolf Jaenisch, Haoyi Wang, Hui Yang, et al. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell, 2013, 153: 1-9.
[31] Wu Y, Liang D, Li J, et al. Correction of a genetic disease in mouse via use of CRISPR-Cas9. Cell Stem Cell, 2013,13(6): 659-662.
[32] Schwank G, Koo B K, Clevers H, et al. Functional repair of CFTR by CRISPR/Cas9 in intestinal stem cell organoids of cystic fibrosis patients. Cell Stem Cell,2013,13(6): 653-658.
[33] Method of the Year 2011. Nat Methods, 2012, 9(1): 1.
[34] Breakthrough of the year: The runners-up. Science, 2012, 338(6114): 1525-1532.
[35] 张金脉, 任兆瑞. TALENs: 一种新的基因定点修饰技术. 生命科学, 2013, 25(1): 54-59. Jinmai Zhang, Zhaorui Ren. TALENs: A new genome sitespecific modification technology. Chinese Bulletin of Life Sciences, 2013, 25(1): 54-59.
[36] Qiurong Ding, Stephanie N Regan, Yulei Xia, et al. Enhanced efficiency of human pluripotent stem cell genome editing through replacing TALENs with CRISPRs. Cell Stem Cell, 2013, 12(4): 393-394.
[37] Soldner F, Laganière J, Cheng A W, et al. Generation of isogenic pluripotent stem cells differing exclusively at two early onsetp arkinson point mutations. Cell, 2011, 146(2): 318-331.
[38] Gaj T, Gersbach C A, Barbas C F. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol, 2013, 31(7): 397-405.
[39] Hsu P D, Scott D A, Zhang F, et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol, 2013, 31(9): 827-832.
[40] Shalem O, Sanjana N E, Zhang F, et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science, 2014,343(6166): 84-87. |
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
| |
Shared |
|
|
|
|
| |
Discussed |
|
|
|
|
