Molecular screening tools to study arabidopsis transcription factors

Frontiers in Plant Science

Volumn 2, Issue NOV, 2011, Pages

  Wehner, Nora ^a   Weiste, Christoph ^a   Dröge Laser, Wolfgang ^a  

^a UNIVERSITY OF WÜRZBURG   (Germany)

Author keywords

Arabidopsis thaliana; Screening tools; Transcription factor function

Indexed keywords

EID: 84872209940     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2011.00068     Document Type: Article

References (42)

1. Baena-Gonzalez, E., Rolland, F., Thevelein, J. M., and Sheen, J. (2007). A central integrator of transcription networks in plant stress and energy signalling. Nature 448, 938-942.
2. Böttner, S., Iven, T., Carsjens, C. S., and Dröge-Laser, W. (2009). Nuclear accumulation of the ankyrin repeat protein ANK1 enhances the auxin-mediated transcription accomplished by the bZIP transcription factors BZI-1 and BZI-2. Plant J. 58, 914-926.
3. Castrillo, G., Turck, F., Leveugle, M., Lecharny, A., Carbonero, P., Coup-land, G., Paz-Ares, J., and Oñate-Sánchez, L. (2011). Speeding cis-trans regulation discovery by phy-logenomic analyses coupled with screenings of an arrayed library of Arabidopsis transcription factors. PLoS ONE 6, e21524. doi: 10.1371/journal.pone.0021524
4. De Sutter, V., Vanderhaeghen, R., Tille-man, S., Lammertyn, F., Vanhoutte, I., Karimi, M., Inze, D., Goossens, A., and Hilson, P. (2005). Exploration of jasmonate signalling via automated and standardized transient expression assays in tobacco cells. Plant J. 44, 1065-1076.
5. Dobi, K. C., and Winston, F. (2007). Analysis of transcriptional activation at a distance in Saccha-romyces cerevisiae. Mol. Cell. Biol. 27, 5575-5586.
6. Ehlert, A., Weltmeier, F., Wang, X., Mayer, C. S., Smeekens, S., Vicente-Carbajosa, J., and Dröge-Laser, W. (2006). Two-hybrid protein-protein interaction analysis in Arabidopsis protoplasts: establishment of a het-erodimerization mapof group C and group S bZIP transcription factors. Plant J. 46, 890-900.
7. Fields, S., and Song, O. (1989). A novel genetic system to detect protein-protein interactions. Nature 340, 245-246.
8. Fode, B., and Gatz, C. (2009). Chro-matin immunoprecipitation experiments to investigate in vivo binding of Arabidopsis transcription factors to target sequences. Methods Mol. Biol. 479, 261-272.
9. Germann, S., and Gaudin, V. (2011). Mapping in vivo protein-DNA interactions in plants by DamID, a DNA adenine methylation-based method. Methods Mol. Biol. 754, 307-321.
10. Godoy, M., Franco-Zorrilla, J. M., Perez-Perez, J., Oliveros, J. C., Lorenzo, O., and Solano, R. (2011). Improved protein-binding microar-rays for the identification of DNA-binding specificities of transcription factors. Plant J. 66, 700-711.
11. Gong, W., Shen, Y. P., Ma, L. G., Pan, Y., Du, Y. L., Wang, D. H., Yang, J. Y., Hu, L. D., Liu, X. F., Dong, C. X., Ma, L., Chen, Y. H., Yang, X. Y., Gao, Y., Zhu, D., Tan, X., Mu, J. Y., Zhang, D. B., Liu, Y. L., Dinesh-Kumar, S. P., Li, Y., Wang, X. P., Gu, H. Y., Qu, L. J., Bai, S. N., Lu, Y. T., Li, J. Y., Zhao, J. D., Zuo, J., Huang, H., Deng, X. W., and Zhu, Y. X. (2004). Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes. Plant Physiol. 135, 773-782.
12. Guo, A., He, K., Liu, D., Bai, S., Gu, X., Wei, L., and Luo, J. (2005). DATF: a database of Arabidopsis transcription factors. Bioinformatics 21, 2568-2569.
13. Heinekamp, T., Kuhlmann, M., Lenk, A., Strathmann, A., and Dröge-Laser, W. (2002). The tobacco bZIP transcription factor BZI-1 binds to G-box elements in the promoters of phenylpropanoid pathway genes in vitro, but it is not involved in their regulation in vivo. Mol. Genet. Genomics 267, 16-26.
14. Hilson, P. (2006). Cloned sequence repertoires for small- and large-scale biology. Trends Plant Sci. 11, 133-141.
15. Hiratsu, K., Matsui, K., Koyama, T., and Ohme-Takagi, M. (2003). Dominant repression of target genes by chimeric repressors that include the EAR motif, a repression domain, in Arabidopsis. Plant J. 34, 733-739.
16. Ichikawa, T., Nakazawa, M., Kawashima, M., Iizumi, H., Kuroda, H., Kondou, Y., Tsuhara, Y., Suzuki, K., Ishikawa, A., Seki, M., Fujita, M., Motohashi, R., Nagata, N., Takagi, T., Shinozaki, K., and Matsui, M. (2006). The FOX hunting system: an alternative gain-of-function gene hunting technique. Plant J. 48, 974-985.
17. Kaufmann, K., Muino, J. M., Osteras, M., Farinelli, L., Krajewski, P., and Angenent, G. C. (2010). Chro-matin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP). Nat. Protoc. 5, 457-472.
18. Kondou, Y., Higuchi, M., and Matsui, M. (2010). High-throughput characterization of plant gene functions by using gain-of-function technology. Annu. Rev. Plant Biol. 61, 373-393.
19. Kuromori, T., Takahashi, S., Kondou, Y., Shinozaki, K., and Matsui, M. (2009). Phenome analysis in plant species using loss-of-function and gain-of-function mutants. Plant Cell Physiol. 50, 1215-1231.
20. Meng, X., Brodsky, M. H., and Wolfe, S. A. (2005). A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors. Nat. Biotechnol. 23, 988-994.
21. Mitsuda, N., Ikeda, M., Takada, S., Takiguchi, Y., Kondou, Y., Yoshizumi, T., Fujita, M., Shinozaki, K., Mat-sui, M., and Ohme-Takagi, M. (2010). Efficient yeast one-/two-hybrid screening using a library composed only of transcription factors. Plant Cell Physiol. 2145-2151.
22. Mitsuda, N., and Ohme-Takagi, M. (2009). Functional analysis of transcription factors in Arabidopsis. Plant Cell Physiol. 50, 1232-1248.
23. Muino, J. M., Kaufmann, K., Van Ham, R. C., Angenent, G. C., and Krajew-ski, P. (2011). ChIP-seq analysis in R (CSAR): an R package for the statistical detection of protein-bound genomic regions. Plant Methods 7, 11.
24. Nakano, T., Suzuki, K., Fujimura, T., and Shinshi, H. (2006). Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant Physiol. 140, 411-432.
25. Ou, B., Yin, K. Q., Liu, S. N., Yang, Y., Gu, T., Wing Hui, J. M., Zhang, L., Miao, J., Kondou, Y., Matsui, M., Gu, H. Y., and Qu, L. J. (2011). A high-throughput screening system for Arabidopsis transcription factors and its application to med25-dependent transcriptional regulation. Mol. Plant 4, 546-555.
26. Paz-Ares, J. (2002). REGIA, an EU project on functional genomics of transcription factors from Arabidop-sis thaliana. Comp. Funct. Genomics 3, 102-108.
27. Perez-Rodriguez, P., Riano-Pachon, D. M., Correa, L. G., Rensing, S. A., Kersten, B., and Mueller-Roeber, B. (2010). PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res. 38, D822-D827.
28. Ptashne, M. (2005). Regulation of transcription: from lambda to eukaryotes. Trends Biochem. Sci. 30, 275-279.
29. Qu, L. J., and Zhu, Y. X. (2006). Transcription factor families in Ara-bidopsis: major progress and outstanding issues for future research. Curr. Opin. Plant Biol. 9, 544-549.
30. Ramirez, S. R., and Basu, C. (2009). Comparative analyses of plant transcription factor databases. Curr. Genomics 10, 10-17.
31. Riechmann, J. L. (2006). "Transcription factors of Arabidopsis and rice: a genomic perspective" in Regulation of Transcription in Plants, ed. K. D. Grasser (Oxford, UK: Blackwell Publishing Ltd), 28-53.
32. Riechmann, J. L., Heard, J., Martin, G., Reuber, L., Jiang, C., Keddie, J., Adam, L., Pineda, O., Ratcliffe, O. J., Samaha, R. R., Creelman, R., Pilgrim, M., Broun, P., Zhang, J. Z., Ghan-dehari, D., Sherman, B. K., and Yu, G. (2000). Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290, 2105-2110.
33. Schütze, K., Harter, K., and Chaban, C. (2008). Post-translational regulation of plant bZIP factors. Trends Plant Sci. 13, 247-255.
34. Seki, M., and Shinozaki, K. (2009). Functional genomics using RIKEN Arabidopsis thaliana full-length cDNAs. J. Plant Res. 122, 355-366.
35. Singh, H., Lebowitz, J. H., Baldwin, A. S. Jr., and Sharp, P. A. (1988). Molecular cloning of an enhancer binding protein: isolation by screening of an expression library with a recognition site DNA. Cell 52, 415-423.
36. Tuerk, C., and Gold, L. (1990). Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510.
37. Wehner, N., Hartmann, L., Ehlert, A., Böttner, S., Onate-Sanchez, L., and Dröge-Laser, W. (2011). High-throughput protoplast trans activation (PTA) system for the analysis of Arabidopsis transcription factor function. Plant J. doi: 10.1111/j.1365-1313X.2011.04704.x
38. Weiste, C., Iven, T., Fischer, U., Onate-Sanchez, L., and Dröge-Laser, W. (2007). In planta ORFeome analysis by large-scale over-expression of GATEWAY-compatible cDNA clones: screening of ERF transcription factors involved in abiotic stress defense. Plant J. 52, 382-390.
39. Weltmeier, F., Ehlert, A., Mayer, C. S., Dietrich, K., Wang, X., Schütze, K., Alonso, R., Harter, K., Vicente-Carbajosa, J., and Dröge-Laser, W. (2006). Combinatorial control of Arabidopsis proline dehy-drogenase transcription by specific heterodimerisation of bZIP transcription factors. EMBO J. 25, 3133-3143.
40. Xue, G. P. (2005). A CELD-fusion method for rapid determination of the DNA-binding sequence specificity of novel plant DNA-binding proteins. Plant J. 41, 638-649.
41. Yilmaz, A., Mejia-Guerra, M. K., Kurz, K., Liang, X., Welch, L., and Grote-wold, E. (2011). AGRIS: the Ara-bidopsis gene regulatory information server, an update. Nucleic Acids Res. 39, D1118-D1122.
42. Zhai, Z., Sooksa-Nguan, T., and Vata-maniuk, O. K. (2009). Establishing RNA interference as a reverse-genetic approach for gene functional analysis in protoplasts. Plant Physiol. 149, 642-652.