Designing and testing the activities of TAL effector nucleases

Methods in Molecular Biology

Volumn 1114, Issue , 2014, Pages 203-219

  Lin, Yanni ^a   Cradick, Thomas J ^a   Bao, Gang ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Gene modification; Gene targeting; Gene therapy; Genome editing; Scoring algorithm for predicted TALEN activity (SAPTA); Scoring function; Single strand annealing (SSA) assay; T7 endonuclease I (T7E1) mutation detection assay; TALEN; Transcription activator like effector nuclease

Indexed keywords

ANTISENSE OLIGONUCLEOTIDE; GENOMIC DNA; GLUTAMINE; HETERODIMER; HOMODIMER; NUCLEASE; TRANSCRIPTION ACTIVATOR LIKE EFFECTOR NUCLEASE; UNCLASSIFIED DRUG;

ALGORITHM; AMPLICON; ARTICLE; BINDING SITE; CPG ISLAND; DNA BINDING; DNA EXTRACTION; DNA METHYLATION; DNA MODIFICATION; DNA SEQUENCE; ENZYME ACTIVITY; EXON; FREEZE THAWING; GENE; GENE MUTATION; GENE TARGETING; GENETIC TRANSFECTION; HUMAN; HUMAN CELL; LIMIT OF DETECTION; OPEN READING FRAME; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUALITY CONTROL; QUANTITATIVE ANALYSIS; RESTRICTION SITE; SCORING ALGORITHM FOR PREDICTED TALEN ACTIVITY; SCORING SYSTEM; SINGLE STRAND ANNEALING ASSAY; STOP CODON; T7 ENDONUCLEASE GENE; ANALYTIC METHOD; CONTROLLED STUDY; ENZYME ASSAY; GENE CONSTRUCT; GENE LOCUS; GENETIC SCREENING; PROTEIN CLEAVAGE;

DEOXYRIBONUCLEASE I; DNA CLEAVAGE; DNA REPAIR; DNA-BINDING PROTEINS; ENDONUCLEASES; GENE TARGETING; MUTATION; PLASMIDS; TRANSFECTION;

EID: 84922070374     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-761-7_13     Document Type: Article

References (25)

1. Boch J, Scholze H, Schornack S, Landgraf A, Hahn S, Kay S, Lahaye T, Nickstadt A, Bonas U (2009) Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326(5959):1509-1512. doi:10.1126/science. 1178811, 1178811 [pii]
2. Boch J, Bonas U (2009) Xanthomonas AvrBs3 family-type III effectors: discovery and function. Annu Rev Phytopathol 48:419-436. doi:10.1146/annurev- phyto-080508-081936
3. Moscou MJ, Bogdanove AJ (2009) A simple cipher governs DNA recognition by TAL effectors. Science 326(5959):1501. doi:10.1126/science.1178817, 1178817 [pii]
4. Schornack S, Meyer A, Römer P, Jordan T, Lahaye T (2006) Gene-for-gene-mediated recognition of nuclear-targeted AvrBs3-like bacterial effector proteins. J Plant Physiol 163(3):256-272. doi:10.1016/j. jplph.2005.12.001, S0176-1617(05)00462-1 [pii]
5. Cermak T, Doyle EL, Christian M, Wang L, Zhang Y, Schmidt C, Baller JA, Somia NV, Bogdanove AJ, Voytas DF (2011) Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res. doi:10.1093/nar/gkr218, gkr218 [pii]
6. Miller JC, Tan S, Qiao G, Barlow KA, Wang J, Xia DF, Meng X, Paschon DE, Leung E, Hinkley SJ, Dulay GP, Hua KL, Ankoudinova I, Cost GJ, Urnov FD, Zhang HS, Holmes MC, Zhang L, Gregory PD, Rebar EJ (2010) A TALE nuclease architecture for efficient genome editing. Nat Biotechnol 29(2):143-148. doi:10.1038/nbt.1755, nbt.1755 [pii]
7. 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 (2011) Knockout rats generated by embryo microinjection of TALENs. Nat Biotechnol 29(8):695-696. doi:10.1038/nbt.1940, nbt.1940 [pii]
8. Christian M, Cermak T, Doyle EL, Schmidt C, Zhang F, Hummel A, Bogdanove AJ, Voytas DF (2010) Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186(2):757-761. doi:10.1534/genetics. 110.120717, genetics.110.120717 [pii]
9. Li T, Huang S, Jiang WZ, Wright D, Spalding MH, Weeks DP, Yang B (2010) TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain. Nucleic Acids Res 39(1):359-372. doi:10.1093/nar/gkq704, gkq704 [pii]
10. Mahfouz MM, Li L, Shamimuzzaman M, Wibowo A, Fang X, Zhu JK (2011) De novo-engineered transcription activator-like effector (TALE) hybrid nuclease with novel DNA binding specificity creates double-strand breaks. Proc Natl Acad Sci USA 108(6):2623-2628. doi:10.1073/pnas.1019533108, 1019533108 [pii]
11. Wood AJ, Lo TW, Zeitler B, Pickle CS, Ralston EJ, Lee AH, Amora R, Miller JC, Leung E, Meng X, Zhang L, Rebar EJ, Gregory PD, Urnov FD, Meyer BJ (2011) Targeted genome editing across species using ZFNs and TALENs. Science 333(6040):307. doi:10.1126/science. 1207773, science.1207773 [pii]
12. Sander JD, Cade L, Khayter C, Reyon D, Peterson RT, Joung JK, Yeh JR (2011) Targeted gene disruption in somatic zebrafish cells using engineered TALENs. Nat Biotechnol 29(8):697-698. doi:10.1038/nbt.1934, nbt.1934 [pii]
13. Huang P, Xiao A, Zhou M, Zhu Z, Lin S, Zhang B (2011) Heritable gene targeting in zebrafish using customized TALENs. Nat Biotechnol 29(8):699-700. doi:10.1038/nbt.1939, nbt.1939 [pii]
14. Mussolino C, Morbitzer R, Lütge F, Dannemann N, Lahaye T, Cathomen T (2011) A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity. Nucleic Acids Res 39(21):9283-9293. doi:10.1093/nar/gkr597, gkr597 [pii]
15. Hockemeyer D, Wang H, Kiani S, Lai CS, Gao Q, Cassady JP, Cost GJ, Zhang L, Santiago Y, Miller JC, Zeitler B, Cherone JM, Meng X, Hinkley SJ, Rebar EJ, Gregory PD, Urnov FD, Jaenisch R (2011) Genetic engineering of human pluripotent cells using TALE nucleases. Nat Biotechnol 29(8):731-734. doi:10.1038/nbt.1927, nbt.1927 [pii]
16. Lin Y, Fine EJ, Zheng Z, Antico CJ, Voit RA, Porteus MH, Cradick TJ, Bao G (in press) SAPTA: a new design tool for improving TALE nuclease activity. Nucleic Acids Research
17. Porteus MH (2006) Mammalian gene targeting with designed zinc finger nucleases. Mol Ther 13(2):438-446. doi:10.1016/j. ymthe.2005.08.003
18. Guschin DY, Waite AJ, Katibah GE, Miller JC, Holmes MC, Rebar EJ (2010) A rapid and general assay for monitoring endogenous gene modification. Methods Mol Biol 649:247-256. doi:10.1007/978-1-60761-753-2-15
19. Zhang F, Cong L, Lodato S, Kosuri S, Church GM, Arlotta P (2011) Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nat Biotechnol 29(2):149-153. doi:10.1038/nbt.1775, nbt.1775 [pii]
20. Briggs AW, Rios X, Chari R, Yang L, Zhang F, Mali P, Church GM (2012) Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers. Nucleic Acids Res 40(15):e117. doi:10.1093/nar/gks624, gks624 [pii]
21. Reyon D, Tsai SQ, Khayter C, Foden JA, Sander JD, Joung JK (2012) FLASH assembly of TALENs for high-throughput genome editing. Nat Biotechnol 30(5):460-465. doi:10.1038/nbt.2170, nbt.2170 [pii]
22. Schmid-Burgk JL, Schmidt T, Kaiser V, Höning K, Hornung V (2013) A ligation-independent cloning technique for high-throughput assembly of transcription activator-like effector genes. Nat Biotechnol 31(1):76-81. doi:10.1038/nbt.2460
23. Kim Y, Kweon J, Kim A, Chon JK, Yoo JY, Kim HJ, Kim S, Lee C, Jeong E, Chung E, Kim D, Lee MS, Go EM, Song HJ, Kim H, Cho N, Bang D, Kim JS (2013) A library of TAL effector nucleases spanning the human genome. Nat Biotechnol 31(3):251-258. doi:10.1038/nbt.2517
24. Deng D, Yin P, Yan C, Pan X, Gong X, Qi S, Xie T, Mahfouz M, Zhu JK, Yan N, Shi Y (2012) Recognition of methylated DNA by TAL effectors. Cell Res. doi:10.1038/cr.2012.127, cr2012127 [pii]
25. Valton J, Dupuy A, Daboussi F, Thomas S, Maréchal A, Macmaster R, Melliand K, Juillerat A, Duchateau P (2012) Overcoming transcription activator-like effector (TALE) DNA binding domain sensitivity to cytosine methylation. The Journal of biological chemistry 287(46):38427-38432. doi:10.1074/jbc. C112.408864