Research Progresses in Gene Editing Techniques

doi:10.13560/j.cnki.biotech.bull.1985.2017-1168

Abstract

Abstract: Gene editing is a powerful set of techniques for site-directed modification and knockout or insertion of the genes on genome or its transcripts. Recently,gene editing techniques have been greatly developed,which not only significantly promotes the process of gene function investigation,but also shows the potential applications for human genetic disease treatments. Here,we summarized the principles,advantages,disadvantages,and applications of gene editing methods including CRISPR/Cas9,CRISPR/Cpf1,Ago/gDNA and SGN in order to provide necessary informations on gene editing for the relevant scientific research.

Key words: Gene editing, CRISPR/Cas9, CRISPR/Cpf1, Ago/gDNA, Structure-guided Nuclease

LIU Yu-biao, XU Xin, CAO Shan-hu, SUN Shao-guang. Research Progresses in Gene Editing Techniques[J]. Biotechnology Bulletin, 2017, 33(6): 39-44.

References

[1] Plump AS, Smith JD, Hayek T, et al. Severe hypercholesterolemia and atherosclerosis in apolipoprotein E deficient mice created by homologous recombination in ES cells[J]. Cell, 1992, 71（2）：343-353.
[2] Capecchi MR. Altering the genome by homologous recombination [J]. Science, 1989, 244（4910）：1288-1292.
[3] Wood AJ, Lo TW, Zeitler B, et al. Targeted genome editing across species using ZFNs and TALENs[J]. Science, 2011, 333（6040）：307-307.
[4] Lo TW, Pickle CS, Lin S, et al. Precise and heritable genome editing in evolutionarily diverse nematodes using TALENs and CRISPR/Cas9 to engineer insertions and deletions[J]. Genetics, 2013, 195（2）：331-348.
[5] Urnov FD, Miller JC, Lee YL, et al. Highly efficient endogenous human gene correction using designed zinc-finger nucleases[J]. Nature, 2005, 435（7042）：646-651.
[6] Miller JC, Holmes MC, Wang J, et al. An improved zinc-finger nuclease architecture for highly specific genome editing[J]. Nat Biotechnol, 2007, 25（7）：778-785.
[7] Boch J, Scholze H, Schornack S, et al. Breaking the code of DNA binding specificity of TAL-type Ⅲ effectors[J]. Science, 2009, 326（5959）：1509-1512.
[8] Jinek M, Chylinski K, Fonfara I, et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity[J]. Science, 2012, 337（6069）：816-821.
[9] Hsu PD, Lander ES, Zhang F. Development and applications of crispr-cas9 for genome engineering[J]. Cell, 2014, 157（6）：1262-1278.
[10] Chylinski K, Le Rhun A, Charpentier E. The tracrRNA and Cas9 families of type Ⅱ CRISPR/Cas immunity systems[J]. RNA Biol, 2013, 10（5）：726-737.
[11] Niu Y, Shen B, Cui Y, et al. Generation of gene-modified cynomolgus monkey via Cas9/RNA-mediated gene targeting in one-cell embryos[J]. Cell, 2014, 156（4）：836-843.
[12] Liang P, Xu Y, Zhang X, et al. CRISPR/Cas9-mediated gene editing in human tripronuclear zygotes[J]. Protein Cell, 2015, 6（5）：363-372.
[13] Kang X, He W, Huang Y, et al. Introducing precise genetic modifications into human 3PN embryos by CRISPR/Cas-mediated genome editing[J]. J Assist Reprod Gen, 2016, 33（5）：581-588.
[14] Zhu S, Li W, Liu J, et al. Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR-Cas9 library[J]. Nat Biotechnol, 2016, 34（12）：1279-1286.
[15] Cyranoski D. CRISPR gene-editing tested in a person for the first time[J]. Nature, 2016, 539（7630）：479.
[16] Zetsche B, Gootenberg JS, Abudayyeh OO, et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system[J]. Cell, 2015, 163（3）：759-771.
[17] Dong D, Ren K, Qiu X, et al. The crystal structure of Cpf1 in complex with CRISPR RNA[J]. Nature, 2016, 532（7600）：522-526.
[18] Mali P, Aach J, Stranges PB, et al. CAS9 transcriptional activators for target specificity screening and paried nickases for cooperative genome engineering[J]. Nat Biotechnol, 2013, 31（9）：833-838.
[19] Kim D, Kim J, Hur JK, et al. Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells[J]. Nat Biotechnol, 2016, 34（8）：863-868.
[20] Song JJ, Smith KK, Hannon GJ, et al. Crystal structure of Argonaute and its implications for RISC slicer activity[J]. Science, 2004, 305（5689）：1434-1437.
[21] Yuan YR, Pei Y, Ma JB, et al. Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC- mediated MRNA cleavage[J]. Mol Cell, 2005, 19（3）：405-419.
[22] Junho KH, Ivan O, Alexei AA. Prokaryotic Argonautes defend genomes against invasive DNA[J]. Trend Biochem Sci, 2014, 39（6）：257-259.
[23] Meister G. Argonaute protein：Functinal insights and emerging roles[J]. Nat Rev Genet, 2013, 14（7）：447-459.
[24] Swarts DC, Jore MM, Westra ER, et al. DNA-guided DNA interference by a prokaryotic Argonaute[J]. Nature, 2014, 507（7491）：258-261.
[25] Daan CS, Jorrit WH, Ismael H, et al. Argonaute of the archaeon Pyrococcus furiosus is a DNA-guided nuclease that targets cognate DNA[J]. Nucleic Acids Res, 2015, 43（10）：5120-5129.
[26] Gao F, Shen XZ, Jiang F, et al. DNA-guided genome editing using the Natronobacterium gregoryi Argonaute[J]. Nat Biotechnol, 2016, 34（7）：768-773.
[27] Qi J, Dong Z, Shi Y, et al. NgAgo-based fabp11a gene knockdown causes eye developmental defects in zebrafish[J]. Cell Res, 2016, 26（12）：1349-1352.
[28] Burgess S, Cheng L, Gu F, et al. Questions about NgAgo[J]. Protein Cell, 2016, 7（12）：913-915.
[29] Lee SH, Turchiano G, Ata H, et al. Failure to detect DNA-guided genome editing using Natronobacterium gregoryi Argonaute[J]. Nat Biotechnol, 2016, 35（1）：17-18.
[30] Imanishi M, Nakamura A, Morisaki T, et al. Positive and negative cooperativity of modularly assembled zinc fingers[J]. Biochem Bioph Res Co, 2009, 387（3）： 440-443.
[31] Maeder ML, Thibodeau-Beganny S, Osiak A, et al. Rapid “open-source” engineering of customized zinc-finger nucleases for highly efficient gene modification[J]. Mol Cell, 2008, 31（2）：294-301.
[32] Juillerat A, Dubois G, Valton J, et al. Comprehensive analysis of the specificity of transcription activator-like effector nucleases[J]. Nucleic Acids Res, 2014, 42（8）：5390-5402.
[33] Smith J, Grizot S, Arnould S, et al. A combinatorial approach to create artificial homing endonucleases cleaving chosen sequences[J]. Nucleic Acids Res, 2006, 34（22）：e149.
[34] Harrington JJ, Lieber MR. The characterization of a mammalian DNA structure-specific endonuclease[J]. EMBO J, 1994, 13（5）：1235-1246.
[35] Kaiser MW, Lyamicheva N, Ma W, et al. A comparison of eubacterial and archaeal structure-specific 5'-exonucleases[J]. J Biol Chem, 1999, 274（30）：21387-21394.
[36] Kao HI, Henricksen LA, Liu Y, et al. Cleavage specificity of Saccharomyces cerevisiae flap endonuclease 1 suggests a double-flap structure as the cellular substrate[J]. J Biol Chem, 2002, 277（17）：14379-14389.
[37] Xu S, Cao S, Zou B, et al. An alternative novel tool for DNA editing without target sequence limitation：the structure-guided nuclease[J]. Genome Biol, 2016, 17（1）：186.
[38] Isabella Wolcott. Could the CRISPR-Cas9 genome editing system be replaced by the NgAgo-gDNA system? [J]. Express Biology, 2016, 1（1）：10-15.