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PLOS ONE  2013 

Rapid Assembly of Customized TALENs into Multiple Delivery Systems

DOI: 10.1371/journal.pone.0080281

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Abstract:

Transcriptional activator-like effector nucleases (TALENs) have become a powerful tool for genome editing. Here we present an efficient TALEN assembly approach in which TALENs are assembled by direct Golden Gate ligation into Gateway? Entry vectors from a repeat variable di-residue (RVD) plasmid array. We constructed TALEN pairs targeted to mouse Ddx3 subfamily genes, and demonstrated that our modified TALEN assembly approach efficiently generates accurate TALEN moieties that effectively introduce mutations into target genes. We generated “user friendly” TALEN Entry vectors containing TALEN expression cassettes with fluorescent reporter genes that can be efficiently transferred via Gateway (LR) recombination into different delivery systems. We demonstrated that the TALEN Entry vectors can be easily transferred to an adenoviral delivery system to expand application to cells that are difficult to transfect. Since TALENs work in pairs, we also generated a TALEN Entry vector set that combines a TALEN pair into one PiggyBac transposon-based destination vector. The approach described here can also be modified for construction of TALE transcriptional activators, repressors or other functional domains.

References

[1]  Friddle CJ, Abuin A, Ramirez-Solis R, Richter LJ, Buxton EC et al. (2003) High-throughput mouse knockouts provide a functional analysis of the genome. Cold Spring Harb Symp Quant Biol 68: 311-315. doi:10.1101/sqb.2003.68.311. PubMed: 15338631.
[2]  Zambrowicz BP, Sands AT (2003) Knockouts model the 100 best-selling drugs--will they model the next 100? Nat Rev Drug Discov 2: 38-51. doi:10.1038/nrd987. PubMed: 12509758.
[3]  Gaj T, Gersbach CA, Barbas CF 3rd (2013) ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol, 31: 397–405. PubMed: 23664777.
[4]  Doyle EL, Stoddard BL, Voytas DF, Bogdanove AJ (2013) TAL effectors: highly adaptable phytobacterial virulence factors and readily engineered DNA-targeting proteins. Trends Cell Biol, 23: 390–8. PubMed: 23707478.
[5]  Sun N, Zhao H (2013) Transcription activator-like effector nucleases (TALENs): A highly efficient and versatile tool for genome editing. Biotechnol Bioeng, 110: 1811–21. PubMed: 23508559.
[6]  Sung YH, Baek IJ, Seong JK, Kim JS, Lee HW (2012) Mouse genetics: catalogue and scissors. BMB Rep 45: 686-692. doi:10.5483/BMBRep.2012.45.12.242. PubMed: 23261053.
[7]  Cathomen T, Joung JK (2008) Zinc-finger nucleases: the next generation emerges. Mol Ther 16: 1200-1207. doi:10.1038/mt.2008.114. PubMed: 18545224.
[8]  Takeuchi R, Lambert AR, Mak AN, Jacoby K, Dickson RJ et al. (2011) Tapping natural reservoirs of homing endonucleases for targeted gene modification. Proc Natl Acad Sci U S A 108: 13077-13082. doi:10.1073/pnas.1107719108. PubMed: 21784983.
[9]  Baxter S, Lambert AR, Kuhar R, Jarjour J, Kulshina N et al. (2012) Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases. Nucleic Acids Res 40: 7985-8000. doi:10.1093/nar/gks502. PubMed: 22684507.
[10]  Taylor GK, Petrucci LH, Lambert AR, Baxter SK, Jarjour J et al. (2012) LAHEDES: the LAGLIDADG homing endonuclease database and engineering server. Nucleic Acids Res 40: W110-W116. doi:10.1093/nar/gks326. PubMed: 22570419.
[11]  Jacoby K, Metzger M, Shen BW, Certo MT, Jarjour J et al. (2012) Expanding LAGLIDADG endonuclease scaffold diversity by rapidly surveying evolutionary sequence space. Nucleic Acids Res 40: 4954-4964. doi:10.1093/nar/gkr1303. PubMed: 22334611.
[12]  Boch J, Scholze H, Schornack S, Landgraf A, Hahn S et al. (2009) Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326: 1509-1512. doi:10.1126/science.1178811. PubMed: 19933107.
[13]  Moscou MJ, Bogdanove AJ (2009) A simple cipher governs DNA recognition by TAL effectors. Science 326: 1501. doi:10.1126/science.1178817. PubMed: 19933106.
[14]  Bogdanove AJ, Voytas DF (2011) TAL effectors: customizable proteins for DNA targeting. Science 333: 1843-1846. doi:10.1126/science.1204094. PubMed: 21960622.
[15]  Sanjana NE, Cong L, Zhou Y, Cunniff MM, Feng G et al. (2012) A transcription activator-like effector toolbox for genome engineering. Nat Protoc 7: 171-192. doi:10.1038/nprot.2011.431. PubMed: 22222791.
[16]  Reyon D, Tsai SQ, Khayter C, Foden JA, Sander JD et al. (2012) FLASH assembly of TALENs for high-throughput genome editing. Nat Biotechnol 30: 460-465. doi:10.1038/nbt.2170. PubMed: 22484455.
[17]  Mussolino C, Morbitzer R, Lütge F, Dannemann N, Lahaye T et al. (2011) A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity. Nucleic Acids Res 39: 9283-9293. doi:10.1093/nar/gkr597. PubMed: 21813459.
[18]  Cermak T, Doyle EL, Christian M, Wang L, Zhang Y et al. (2011) Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res 39: e82. doi:10.1093/nar/gkr218. PubMed: 21493687.
[19]  Sun N, Liang J, Abil Z, Zhao H (2012) Optimized TAL effector nucleases (TALENs) for use in treatment of sickle cell disease. Mol Biosyst 8: 1255-1263. doi:10.1039/c2mb05461b. PubMed: 22301904.
[20]  Miller JC, Tan S, Qiao G, Barlow KA, Wang J et al. (2011) A TALE nuclease architecture for efficient genome editing. Nat Biotechnol 29: 143-148. doi:10.1038/nbt.1755. PubMed: 21179091.
[21]  Chen S, Oikonomou G, Chiu CN, Niles BJ, Liu J et al. (2013) A large-scale in vivo analysis reveals that TALENs are significantly more mutagenic than ZFNs generated using context-dependent assembly. Nucleic Acids Res 41: 2769-2778. doi:10.1093/nar/gks1356. PubMed: 23303782.
[22]  Zhang Y, Zhang F, Li X, Baller JA, Qi Y et al. (2013) Transcription activator-like effector nucleases enable efficient plant genome engineering. Plant Physiol 161: 20-27. doi:10.1104/pp.112.205179. PubMed: 23124327.
[23]  Li T, Liu B, Spalding MH, Weeks DP, Yang B (2012) High-efficiency TALEN-based gene editing produces disease-resistant rice. Nat Biotechnol 30: 390-392. doi:10.1038/nbt.2199. PubMed: 22565958.
[24]  Li T, Huang S, Zhao X, Wright DA, Carpenter S et al. (2011) Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes. Nucleic Acids Res 39: 6315-6325. doi:10.1093/nar/gkr188. PubMed: 21459844.
[25]  Liu J, Li C, Yu Z, Huang P, Wu H et al. (2012) Efficient and specific modifications of the Drosophila genome by means of an easy TALEN strategy. J Genet Genomics 39: 209-215. doi:10.1016/j.jgg.2012.04.003. PubMed: 22624882.
[26]  Ansai S, Sakuma T, Yamamoto T, Ariga H, Uemura N et al. (2013) Efficient targeted mutagenesis in medaka using custom-designed transcription activator-like effector nucleases. Genetics 193: 739-749. doi:10.1534/genetics.112.147645. PubMed: 23288935.
[27]  Zu Y, Tong X, Wang Z, Liu D, Pan R et al. (2013) TALEN-mediated precise genome modification by homologous recombination in zebrafish. Nat Methods 10: 329-331. doi:10.1038/nmeth.2374. PubMed: 23435258.
[28]  Moore FE, Reyon D, Sander JD, Martinez SA, Blackburn JS et al. (2012) Improved somatic mutagenesis in zebrafish using transcription activator-like effector nucleases (TALENs). PLOS ONE 7: e37877. doi:10.1371/journal.pone.0037877. PubMed: 22655075.
[29]  Sakuma T, Hosoi S, Woltjen K, Suzuki K, Kashiwagi K et al. (2013) Efficient TALEN construction and evaluation methods for human cell and animal applications. Genes Cells 18: 315-326. doi:10.1111/gtc.12037. PubMed: 23388034.
[30]  Cristea S, Freyvert Y, Santiago Y, Holmes MC, Urnov FD et al. (2013) In vivo cleavage of transgene donors promotes nuclease-mediated targeted integration. Biotechnol Bioeng 110: 871-880. doi:10.1002/bit.24733. PubMed: 23042119.
[31]  Wang H, Hu YC, Markoulaki S, Welstead GG, Cheng AW et al. (2013) TALEN-mediated editing of the mouse Y chromosome. Nat Biotechnol, 31: 530–2. PubMed: 23666012.
[32]  Bedell VM, Wang Y, Campbell JM, Poshusta TL, Starker CG et al. (2012) In vivo genome editing using a high-efficiency TALEN system. Nature 491: 114-118. doi:10.1038/nature11537. PubMed: 23000899.
[33]  Sung YH, Baek IJ, Kim DH, Jeon J, Lee J et al. (2013) Knockout mice created by TALEN-mediated gene targeting. Nat Biotechnol 31: 23-24. doi:10.1038/nbt.2477. PubMed: 23302927.
[34]  Tesson L, Usal C, Ménoret S, Leung E, Niles BJ et al. (2011) Knockout rats generated by embryo microinjection of TALENs. Nat Biotechnol 29: 695-696. doi:10.1038/nbt.1940. PubMed: 21822240.
[35]  Carlson DF, Tan W, Lillico SG, Stverakova D, Proudfoot C et al. (2012) Efficient TALEN-mediated gene knockout in livestock. Proc Natl Acad Sci U S A 109: 17382-17387. doi:10.1073/pnas.1211446109. PubMed: 23027955.
[36]  Kim Y, Kweon J, Kim A, Chon JK, Yoo JY et al. (2013) A library of TAL effector nucleases spanning the human genome. Nat Biotechnol 31: 251-258. doi:10.1038/nbt.2517. PubMed: 23417094.
[37]  Ding Q, Lee YK, Schaefer EA, Peters DT, Veres A et al. (2013) A TALEN genome-editing system for generating human stem cell-based disease models. Cell Stem Cell 12: 238-251. doi:10.1016/j.stem.2012.11.011. PubMed: 23246482.
[38]  Schmid-Burgk JL, Schmidt T, Kaiser V, H?ning K, Hornung V (2013) A ligation-independent cloning technique for high-throughput assembly of transcription activator-like effector genes. Nat Biotechnol 31: 76-81. PubMed: 23242165.
[39]  Stroud DA, Formosa LE, Wijeyeratne XW, Nguyen TN, Ryan MT (2013) Gene knockout using transcription activator-like effector nucleases (TALENs) reveals that human NDUFA9 protein is essential for stabilizing the junction between membrane and matrix arms of complex I. J Biol Chem 288: 1685-1690. doi:10.1074/jbc.C112.436766. PubMed: 23223238.
[40]  Choi SM, Kim Y, Shim JS, Park JT, Wang RH et al. (2013) Efficient drug screening and gene correction for treating liver disease using patient-specific stem cells. Hepatology, 57: 2458–68. PubMed: 23325555.
[41]  Zhang F, Cong L, Lodato S, Kosuri S, Church GM et al. (2011) Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nat Biotechnol 29: 149-153. doi:10.1038/nbt.1775. PubMed: 21248753.
[42]  Geissler R, Scholze H, Hahn S, Streubel J, Bonas U et al. (2011) Transcriptional activators of human genes with programmable DNA-specificity. PLOS ONE 6: e19509. doi:10.1371/journal.pone.0019509. PubMed: 21625585.
[43]  Cong L, Zhou R, Kuo YC, Cunniff M, Zhang F (2012) Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains. Nat Commun 3: 968. doi:10.1038/ncomms1962. PubMed: 22828628.
[44]  Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA et al. (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337: 816-821. doi:10.1126/science.1225829. PubMed: 22745249.
[45]  Mali P, Yang L, Esvelt KM, Aach J, Guell M et al. (2013) RNA-guided human genome engineering via Cas9. Science 339: 823-826. doi:10.1126/science.1232033. PubMed: 23287722.
[46]  Cong L, Ran FA, Cox D, Lin S, Barretto R et al. (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339: 819-823. doi:10.1126/science.1231143. PubMed: 23287718.
[47]  Wang H, Yang H, Shivalila CS, Dawlaty MM, Cheng AW et al. (2013) One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering. Cell, 153: 910–8. PubMed: 23643243.
[48]  Fu Y, Foden JA, Khayter C, Maeder ML, Reyon D et al. (2013) High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Biotechnol, 31: 822–6. PubMed: 23792628.
[49]  Engler C, Marillonnet S (2011) Generation of families of construct variants using golden gate shuffling. Methods Mol Biol 729: 167-181. doi:10.1007/978-1-61779-065-2_11. PubMed: 21365490.
[50]  Walhout AJ, Temple GF, Brasch MA, Hartley JL, Lorson MA et al. (2000) GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes. Methods Enzymol 328: 575-592. doi:10.1016/S0076-6879(00)28419-X. PubMed: 11075367.
[51]  Hartley JL, Temple GF, Brasch MA (2000) DNA cloning using in vitro site-specific recombination. Genome Res 10: 1788-1795. doi:10.1101/gr.143000. PubMed: 11076863.
[52]  Holkers M, Maggio I, Liu J, Janssen JM, Miselli F et al. (2013) Differential integrity of TALE nuclease genes following adenoviral and lentiviral vector gene transfer into human cells. Nucleic Acids Res 41: e63. doi:10.1093/nar/gks1029. PubMed: 23275534.
[53]  Cheo DL, Titus SA, Byrd DR, Hartley JL, Temple GF et al. (2004) Concerted assembly and cloning of multiple DNA segments using in vitro site-specific recombination: functional analysis of multi-segment expression clones. Genome Res 14: 2111-2120. doi:10.1101/gr.2512204. PubMed: 15489333.
[54]  Uhde-Stone C, Gor N, Chin T, Huang J, Lu B (2013) A do-it-yourself protocol for simple transcription activator-like effector assembly. Biol Proced Online 15: 3. doi:10.1186/1480-9222-15-3. PubMed: 23316790.
[55]  Zhang Z, Li D, Xu H, Xin Y, Zhang T et al. (2013) A simple and efficient method for assembling TALE protein based on plasmid library. PLOS ONE 8: e66459. doi:10.1371/journal.pone.0066459. PubMed: 23840477.
[56]  Weber E, Gruetzner R, Werner S, Engler C, Marillonnet S (2011) Assembly of designer TAL effectors by Golden Gate cloning. PLOS ONE 6: e19722. doi:10.1371/journal.pone.0019722. PubMed: 21625552.
[57]  Christian ML, Demorest ZL, Starker CG, Osborn MJ, Nyquist MD et al. (2012) Targeting G with TAL effectors: a comparison of activities of TALENs constructed with NN and NK repeat variable di-residues. PLOS ONE 7: e45383. doi:10.1371/journal.pone.0045383. PubMed: 23028976.
[58]  Hu R, Wallace J, Dahlem TJ, Grunwald DJ, O'Connell RM (2013) Targeting Human MicroRNA Genes Using Engineered Tal-Effector Nucleases (TALENs). PLOS ONE 8: e63074. doi:10.1371/journal.pone.0063074. PubMed: 23667577.
[59]  Mashimo T, Kaneko T, Sakuma T, Kobayashi J, Kunihiro Y et al. (2013) Efficient gene targeting by TAL effector nucleases coinjected with exonucleases in zygotes. Sci Rep 3: 1253. PubMed: 23409244.
[60]  Davies B, Davies G, Preece C, Puliyadi R, Szumska D et al. (2013) Site Specific Mutation of the Zic2 Locus by Microinjection of TALEN mRNA in Mouse CD1, C3H and C57BL/6J Oocytes. PLOS ONE 8: e60216. doi:10.1371/journal.pone.0060216. PubMed: 23555929.
[61]  Qiu Z, Liu M, Chen Z, Shao Y, Pan H et al. (2013) High-efficiency and heritable gene targeting in mouse by transcription activator-like effector nucleases. Nucleic Acids Res, 41: e120-. PubMed: 23630316.
[62]  Li T, Yang B (2013) TAL effector nuclease (TALEN) engineering. Methods Mol Biol 978: 63-72. doi:10.1007/978-1-62703-293-3_5. PubMed: 23423889.
[63]  Alba R, Bosch A, Chillon M (2005) Gutless adenovirus: last-generation adenovirus for gene therapy. Gene Ther 12 Suppl 1: S18-S27. doi:10.1038/sj.gt.3302612. PubMed: 16231052.
[64]  Li R, Zhuang Y, Han M, Xu T, Wu X (2013) piggyBac as a high-capacity transgenesis and gene-therapy vector in human cells and mice. Dis Model. J Mech 6: 828-833.
[65]  Rostovskaya M, Naumann R, Fu J, Obst M, Mueller D et al. (2013) Transposon mediated BAC transgenesis via pronuclear injection of mouse zygotes. Genesis 51: 135-141. doi:10.1002/dvg.22362. PubMed: 23225373.
[66]  Rostovskaya M, Fu J, Obst M, Baer I, Weidlich S et al. (2012) Transposon-mediated BAC transgenesis in human ES cells. Nucleic Acids Res 40: e150. doi:10.1093/nar/gks643. PubMed: 22753106.
[67]  Li MA, Turner DJ, Ning Z, Yusa K, Liang Q et al. (2011) Mobilization of giant piggyBac transposons in the mouse genome. Nucleic Acids Res 39: e148. doi:10.1093/nar/gkr764. PubMed: 21948799.
[68]  Li M, Izpisua Belmonte JC (2012) No factor left behind: generation of transgene-free induced pluripotent stem cells. Am J Stem Cells 1: 75-80. PubMed: 23671799.
[69]  Li MA, Pettitt SJ, Eckert S, Ning Z, Rice S et al. (2013) The piggyBac transposon displays local and distant reintegration preferences and can cause mutations at noncanonical integration sites. Mol Cell Biol 33: 1317-1330. doi:10.1128/MCB.00670-12. PubMed: 23358416.

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