Context influences on TALE-DNA binding revealed by quantitative profiling

Nature Communications

Volumn 6, Issue , 2015, Pages

  Rogers, Julia M ^a,b   Barrera, Luis A ^a,b,c,d   Reyon, Deepak ^e,f   Sander, Jeffry D ^e,f   Kellis, Manolis ^d   Keith Joung, J ^e,f   Bulyk, Martha L ^a,b,c  

^a BRIGHAM AND WOMEN S HOSPITAL   (United States)

^b HARVARD UNIVERSITY   (United States)

^c HARVARD MIT DIVISION OF HEALTH SCIENCES AND TECHNOLOGY   (United States)

^d MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^e MASSACHUSETTS GENERAL HOSPITAL   (United States)

^f HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; TRANSCRIPTION ACTIVATOR LIKE EFFECTOR PROTEIN; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; DNA BINDING PROTEIN; PROTEIN BINDING;

CHEMICAL BINDING; DNA; GENETIC ENGINEERING; GENOME; GENOMICS; PROTEIN; QUANTITATIVE ANALYSIS;

ARTICLE; DNA BINDING; DNA FINGERPRINTING; DNA MICROARRAY; DNA SEQUENCE; GENE TARGETING; MOLECULAR RECOGNITION; PROTEIN DNA INTERACTION; QUANTITATIVE ANALYSIS; METABOLISM; MOLECULAR MODEL; NUCLEOTIDE SEQUENCE; PROTEIN MICROARRAY;

BASE SEQUENCE; DNA; DNA-BINDING PROTEINS; MODELS, MOLECULAR; PROTEIN ARRAY ANALYSIS; PROTEIN BINDING;

EID: 84931287738     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms8440     Document Type: Article

References (47)

1. Byrum, S. D., Taverna, S. D., Tackett, A. J. Purification of a specific native genomic locus for proteomic analysis. Nucleic Acids Res. 41, e195 (2013).
2. Joung, J. K., Sander, J. D. TALENs: a widely applicable technology for targeted genome editing. Nat. Rev. Mol. Cell Biol. 14, 49-55 (2013).
3. Maeder, M. L. et al. Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins. Nature Biotechnol. 31, 1137-1142 (2013).
4. Maeder, M. L. et al. Robust, synergistic regulation of human gene expression using TALE activators. Nat. Methods 10, 243-245 (2013).
5. Mendenhall, E. M. et al. Locus-specific editing of histone modifications at endogenous enhancers. Nature Biotechnol. 31, 1133-1136 (2013).
6. Cong, L., Zhou, R., Kuo, Y. C., Cunniff, M., Zhang, F. Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains. Nat. Commun. 3, 968 (2012).
7. Miyanari, Y., Ziegler-Birling, C., Torres-Padilla, M. E. Live visualization of chromatin dynamics with fluorescent TALEs. Nat. Struct. Mol. Biol. 20, 1321-1324 (2013).
8. Perez-Pinera, P. et al. Synergistic and tunable human gene activation by combinations of synthetic transcription factors. Nat. Methods 10, 239-242 (2013).
9. Moscou, M. J., Bogdanove, A. J. A simple cipher governs DNA recognition by TAL effectors. Science 326, 1501 (2009).
10. Boch, J. et al. Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326, 1509-1512 (2009).
11. Mak, A. N., Bradley, P., Cernadas, R. A., Bogdanove, A. J., Stoddard, B. L. The crystal structure of TAL effector PthXo1 bound to its DNA target. Science 335, 716-719 (2012).
12. Deng, D. et al. Structural basis for sequence-specific recognition of DNA by TAL effectors. Science 335, 720-723 (2012).
13. Stella, S. et al. Structure of the AvrBs3-DNA complex provides new insights into the initial thymine-recognition mechanism. Acta Crystallogr. D Biol. Crystallogr. 69, 1707-1716 (2013).
14. Doudna, J. A., Charpentier, E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 346, 1258096 (2014).
15. Ding, Q. et al. A TALEN genome-editing system for generating human stem cell-based disease models. Cell Stem Cell 12, 238-251 (2013).
16. Osborn, M. J. et al. TALEN-based gene correction for epidermolysis bullosa. Mol. Ther. 21, 1151-1159 (2013).
17. Tesson, L. et al. Knockout rats generated by embryo microinjection of TALENs. Nat. Biotechnol. 29, 695-696 (2011).
18. Hockemeyer, D. et al. Genetic engineering of human pluripotent cells using TALE nucleases. Nature Biotechnol. 29, 731-734 (2011).
19. Mussolino, C. et al. A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity. Nucleic Acids Res. 39, 9283-9293 (2011).
20. Guilinger, J. P. et al. Broad specificity profiling of TALENs results in engineered nucleases with improved DNA-cleavage specificity. Nat. Methods 11, 429-435 (2014).
21. Morbitzer, R., Römer, P., Boch, J., Lahaye, T. Regulation of selected genome loci using de novo-engineered transcription activator-like effector (TALE)-type transcription factors. Proc. Natl Acad. Sci. USA 107, 21617-21622 (2010).
22. Mali, P. et al. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nature Biotechnol. 31, 833-838 (2013).
23. Doyle, E. L. et al. TAL Effector-Nucleotide Targeter (TALE-NT) 2. 0: tools for TAL effector design and target prediction. Nucleic Acids Res. 40, W117-W122 (2012).
24. Grau, J. et al. Computational predictions provide insights into the biology of TAL effector target sites. PLoS Comput. Biol. 9, e1002962 (2013).
25. Meckler, J. F. et al. Quantitative analysis of TALE-DNA interactions suggests polarity effects. Nucleic Acids Res. 41, 4118-4128 (2013).
26. Streubel, J., Blucher, C., Landgraf, A., Boch, J. TAL effector RVD specificities and efficiencies. Nature Biotechnol. 30, 593-595 (2012).
27. Fine, E. J., Cradick, T. J., Zhao, C. L., Lin, Y., Bao, G. An online bioinformatics tool predicts zinc finger and TALE nuclease off-target cleavage. Nucleic Acids Res. 42, e42 (2014).
28. Perez-Quintero, A. L. et al. An improved method for TAL effectors DNAbinding sites prediction reveals functional convergence in TAL repertoires of Xanthomonas oryzae strains. PLoS ONE 8, e68464 (2013).
29. Berger, M. F., Bulyk, M. L. Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nat. Protoc. 4, 393-411 (2009).
30. Berger, M. F. et al. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nature Biotechnol. 24, 1429-1435 (2006).
31. Mukherjee, S. et al. Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nature Genet. 36, 1331-1339 (2004).
32. Reyon, D. et al. FLASH assembly of TALENs for high-throughput genome editing. Nature Biotechnol. 30, 460-465 (2012).
33. Siggers, T., Duyzend, M. H., Reddy, J., Khan, S., Bulyk, M. L. Non-DNAbinding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex. Mol. Syst. Biol. 7, 555 (2011).
34. Zou, H., Hastie, T. Regularization and variable selection via the elastic net. J. R. Statist. Soc. B 67, 301-320 (2005).
35. Juillerat, A. et al. Comprehensive analysis of the specificity of transcription activator-like effector nucleases. Nucleic Acids Res. 42, 5390-5402 (2014).
36. Zhao, Y., Stormo, G. D. Quantitative analysis demonstrates most transcription factors require only simple models of specificity. Nature Biotechnol. 29, 480-483 (2011).
37. Garg, A., Lohmueller, J. J., Silver, P. A., Armel, T. Z. Engineering synthetic TAL effectors with orthogonal target sites. Nucleic Acids Res. 40, 7584-7595 (2012).
38. Schreiber, T., Bonas, U. Repeat 1 of TAL effectors affects target specificity for the base at position zero. Nucleic Acids Res. 42, 7160-7169 (2014).
39. Blankenberg, D. et al. Galaxy: a web-based genome analysis tool for experimentalists. Curr. Protoc. Mol. Biol. Chapter 19, Unit 19 10 11-Unit 19 10 21 (2010).
40. Giardine, B. et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 15, 1451-1455 (2005).
41. Goecks, J., Nekrutenko, A., Taylor, J., Galaxy, T. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11, R86 (2010).
42. Gu, K. et al. R gene expression induced by a type-III effector triggers disease resistance in rice. Nature 435, 1122-1125 (2005).
43. Lin, Y. et al. SAPTA: a new design tool for improving TALE nuclease activity. Nucleic Acids Res. 42, e47 (2014).
44. Siggers, T. et al. Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-kappaB family DNA binding. Nature Immunol. 13, 95-102 (2012).
45. Dudley, A. M., Aach, J., Steffen, M. A., Church, G. M. Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc. Natl Acad. Sci. USA 99, 7554-7559 (2002).
46. Lee, P. M. Bayesian Statistics: An Introduction (1997).
47. Hoffman, M. D., Gelman, A. The No-U-Turn Sampler: Adaptively Setting Path Lengths in Hamiltonian Monte Carlo. arXiv:1111. 4246 [stat. CO] (2011).