Multiplex genomic structure variation mediated by TALEN and ssODN

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Ma, Sanyuan ^a   Wang, Xiaogang ^a   Liu, Yuanyuan ^a   Gao, Jie ^a   Zhang, Shengling ^a   Shi, Run ^a   Chang, Jiasong ^a   Zhao, Ping ^a   Xia, Qingyou ^a  

^a SOUTHWEST UNIVERSITY   (China)

Author keywords

Chromosomal deletion; Chromosomal duplication; Chromosomal inversion; Genomic structure variation; ssODN; TAL Effectors

Indexed keywords

ENDONUCLEASE; MESSENGER RNA; OLIGODEOXYRIBONUCLEOTIDE;

ALGORITHM; ANIMAL; BOMBYX; CHEMISTRY; CHROMOSOME; CHROMOSOME DELETION; CHROMOSOME DUPLICATION; CHROMOSOME INVERSION; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; GENOME; METABOLISM; NUCLEOTIDE SEQUENCE; SYNTHESIS;

ALGORITHMS; ANIMALS; BASE SEQUENCE; BOMBYX; CHROMOSOME DELETION; CHROMOSOME DUPLICATION; CHROMOSOME INVERSION; CHROMOSOMES; ENDONUCLEASES; GENOME; GENOMIC STRUCTURAL VARIATION; OLIGODEOXYRIBONUCLEOTIDES; RNA, MESSENGER; SEQUENCE ANALYSIS, DNA;

EID: 84892468621     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-41     Document Type: Article

References (33)

1. Korbel J, Urban A, Affourtit J, Godwin B, Grubert F, Simons J, Kim P, Palejev D, Carriero N, Du L, Taillon BE, Chen Z, Tanzer A, Saunders AC, Chi J, Yang F, Carter NP, Hurles ME, Weissman SM, Harkins TT, Gerstein MB, Egholm M, Snyder M. Paired-end mapping reveals extensive structural variation in the human genome. Science 2007, 318:420-426. 10.1126/science.1149504, 2674581, 17901297.
2. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, González JR, Gratacòs M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, et al. Global variation in copy number in the human genome. Nature 2006, 444:444-454. 10.1038/nature05329, 2669898, 17122850.
3. Stephens PJ, McBride DJ, Lin ML, Varela I, Pleasance ED, Simpson JT, Stebbings LA, Leroy C, Edkins S, Mudie LJ, Greenman CD, Jia M, Latimer C, Teague JW, Lau KW, Burton J, Quail MA, Swerdlow H, Churcher C, Natrajan R, Sieuwerts AM, Martens JW, Silver DP, Langerød A, Russnes HE, Foekens JA, Reis-Filho JS, Vant Veer L, Richardson AL, Børresen-Dale AL, et al. Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature 2009, 462:1005-1010. 10.1038/nature08645, 3398135, 20033038.
4. Stankiewicz P, Lupski JR. Structural variation in the human genome and its role in disease. Annu Rev Med 2010, 61:437-455. 10.1146/annurev-med-100708-204735, 20059347.
5. Lee HJ, Kweon J, Kim E, Kim S, Kim JS. Targeted chromosomal duplications and inversions in the human genome using zinc finger nucleases. Genome Res 2011, 22:539-548. 3290789, 22183967.
6. Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, Shi X, Fulton RS, Ley TJ, Wilson RK, Ding L, Mardis ER. BreakDancer: An algorithm for high-resolution mapping of genomic structural variation. Nat Methods 2009, 6:677-681. 10.1038/nmeth.1363, 3661775, 19668202.
7. Brunet E, Simsek D, Tomishima M, DeKelver R, Choi VM, Gregory P, Urnov F, Weinstock DM, Jasin M. Chromosomal translocations induced at specified loci in human stem cells. Proc Natl Acad Sci U S A 2009, 106:10620-10625. 10.1073/pnas.0902076106, 2700748, 19549848.
8. Simsek D, Brunet E, Wong SY, Katyal S, Gao Y, McKinnon PJ, Lou J, Zhang L, Li J, Rebar EJ, Gregory PD, Holmes MC, Jasin M. DNA ligase III promotes alternative nonhomologous end-joining during chromosomal translocation formation. PLoS Genet 2011, 7:e1002080. 10.1371/journal.pgen.1002080, 3107202, 21655080.
9. Sargent RG, Kim S, Gruenert DC. Oligo/polynucleotide-based gene modification: strategies and therapeutic potential. Oligonucleotides 2011, 21:55-75. 10.1089/oli.2010.0273, 3078494, 21417933.
10. Joung JH, Sander JD. TALENs: a widely applicable technology for targeted genome editing. Nat Rev Mol Cell Biol 2013, 14:49-55. 3547402, 23169466.
11. Ma S, Zhang S, Wang F, Liu Y, Liu Y, Xu H, Liu C, Lin Y, Zhao P, Xia Q. Highly efficient and specific genome editing in silkworm using custom TALENs. PLoS ONE 2012, 7(9):e45035. 10.1371/journal.pone.0045035, 3445556, 23028749.
12. Carlson DF, Tan W, Lillico SG, Stverakova D, Proudfoot C, Christian M, Voytas DF, Long CR, Whitelaw CB, Fahrenkrug SC. Efficient TALEN-mediated gene knockout in livestock. Proc Natl Acad Sci U S A 2012, 109:17382-17387. 10.1073/pnas.1211446109, 3491456, 23027955.
13. Reyon D, Tsai SQ, Khayter C, Foden JA, Sander JD, Joung JK. FLASH assembly of TALENs for high-throughput genome editing. Nat Biotechnol 2012, 30:460-465. 10.1038/nbt.2170, 3558947, 22484455.
14. Schmid-Burgk JL, Schmidt T, Kaiser V, Höning K, Hornung V. A ligation-independent cloning technique for high-throughput assembly of transcription activator-like effector genes. Nat Biotechnol 2012, 31(1):76-81.
15. Wang Z, Li J, Huang H, Wang G, Jiang M, Yin S, Sun C, Zhang H, Zhuang F, Xi JJ. An integrated chip for the high-throughput synthesis of transcription activator-like effectors. Angew Chem Int Ed Engl 2012, 51:8505-8508. 10.1002/anie.201203597, 22821513.
16. Tesson L, Usal C, Ménoret S, Leung E, Niles BJ, Remy S, Santiago Y, Vincent AI, Meng X, Zhang L, Gregory PD, Anegon I, Cost GJ. Knockout rats generated by embryo microinjection of TALENs. Nat Biotechnol 2011, 29(8):695-696. 10.1038/nbt.1940, 21822240.
17. Chen F, Pruett-Miller SM, Huang Y, Gjoka M, Duda K, Taunton J, Collingwood TN, Frodin M, Davis GD. High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases. Nat Methods 2011, 8:753-755. 10.1038/nmeth.1653, 3617923, 21765410.
18. Sharp AJ, Cheng Z, Eichler EE. Structural variation of the human genome. Annu Rev Genomics Hum Genet 2006, 7:407-442. 10.1146/annurev.genom.7.080505.115618, 16780417.
19. Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nat Rev Genet 2006, 7(2):85-97.
20. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F. Multiplex genome engineering using CRISPR/Cas systems. Science 2013, 339(6121):819-823. 10.1126/science.1231143, 3795411, 23287718.
21. Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM. RNA-guided human genome engineering via Cas9. Science 2013, 339(6121):823-826. 10.1126/science.1232033, 3712628, 23287722.
22. Jinek M, East A, Cheng A, Lin S, Ma E, Doudna J. RNA-programmed genome editing in human cells. Elife 2013, 2:e00471. 10.7554/eLife.00471, 3557905, 23386978.
23. Söllü C, Pars K, Cornu TI, Thibodeau-Beganny S, Maeder ML, Joung JK, Heilbronn R, Cathomen T. Autonomous zinc-finger nuclease pairs for targeted chromosomal deletion. Nucleic Acids Res 2010, 38(22):8269-8276. 10.1093/nar/gkq720, 3001086, 20716517.
24. Lee HJ, Kim E, Kim JS. Targeted chromosomal deletions in human cells using zinc finger nucleases. Genome Res 2010, 20:81-89. 10.1101/gr.099747.109, 2798833, 19952142.
25. Petolino JF, Worden A, Curlee K, Connell J, Strange Moynahan TL, Larsen C, Russell S. Zinc finger nuclease-mediated transgene deletion. Plant Mol Biol 2010, 73(6):617-628. 10.1007/s11103-010-9641-4, 20454835.
26. Gupta A, Hall VL, Kok FO, Shin M, McNulty JC, Lawson ND, Wolfe SA. Targeted chromosomal deletions and inversions in Zebrafish. Genome Res 2013, 23(6):1008-1017. 10.1101/gr.154070.112, 3668355, 23478401.
27. Kim Y, Kweon J, Kim JS. TALENs and ZFNs are associated with different mutation signatures. Nat Methods 2013, 10(3):185. 10.1038/nmeth.2364, 23396284.
28. Orlando SJ, Santiago Y, DeKelver RC, Freyvert Y, Boydston EA, Moehle EA, Choi VM, Gopalan SM, Lou JF, Li J, Miller JC, Holmes MC, Gregory PD, Urnov FD, Cost GJ. Zinc-finger nuclease-driven targeted integration into mammalian genomes using donors with limited chromosomal homology. Nucleic Acids Res 2010, 38(15):e152. 10.1093/nar/gkq512, 2926620, 20530528.
29. Maresca M, Lin VG, Guo N, Yang Y. Obligate Ligation-Gated Recombination (ObLiGaRe): Custom-designed nucleases mediated targeted integration through nonhomologous end joining. Genome Res 2013, 23(3):539-546. 10.1101/gr.145441.112, 3589542, 23152450.
30. Holt N, Wang J, Kim K, Friedman G, Wang X, Taupin V, Crooks GM, Kohn DB, Gregory PD, Holmes MC, Cannon PM. Human hematopoietic stem/progenitor cells modified by zinc-finger nucleases targeted to CCR5 control HIV-1 in vivo. Nat Biotechnol 2010, 28:839-847. 10.1038/nbt.1663, 3080757, 20601939.
31. Aarts M, te Riele H. Progress and prospects: oligonucleotide-directed gene modification in mouse embryonic stem cells: a route to therapeutic application. Gene Ther 2011, 18(3):213-219. 10.1038/gt.2010.161, 21160530.
32. Taylor EM, Lehmann AR. Conservation of eukaryotic DNA repair mechanisms. Int J Radiat Biol 1998, 74(3):277-286. 10.1080/095530098141429, 9737531.
33. Cromie GA, Connelly JC, Leach DR. Recombination at double-strand breaks and DNA ends: conserved mechanisms from phage to humans. Mol Cell 2001, 8(6):1163-1174. 10.1016/S1097-2765(01)00419-1, 11779493.