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. 2002 Apr;3(2):102–108. doi: 10.1002/cfg.146

REGIA, An EU Project on Functional Genomics of Transcription Factors From Arabidopsis Thaliana

Javier Paz-Ares 1,✉, The REGIA Consortium 1
PMCID: PMC2447270  PMID: 18628849

Abstract

Transcription factors (TFs) are regulatory proteins that have played a pivotal role in the evolution of eukaryotes and that also have great biotechnological potential. REGIA (REgulatory Gene Initiative in Arabidopsis) is an EU-funded project involving 29 European laboratories with the objective of determining the function of virtually all transcription factors from the model plant, Arabidopsis thaliana. REGIA involves: 1. the definition of TF gene expression patterns in Arabidopsis; 2. the identification of mutations at TF loci; 3. the ectopic expression of TFs (or derivatives) in Arabidopsis and in crop plants; 4. phenotypic analysis of the mutants and mis-expression lines, including both RNA and metabolic profiling; 5. the systematic analysis of interactions between TFs; and 6. the generation of a bioinformatics infrastructure to access and integrate all this information. We expect that this programme will establish the full biotechnological potential of plant TFs, and provide insights into hierarchies, redundancies, and interdependencies, and their evolution. The project involves the preparation of both a TF gene array for expression analysis and a normalised full length open reading frame (ORF) library of TFs in a yeast two hybrid vector; the applications of these resources should extend beyond the scope of this programme.

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Selected References

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  1. Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000 Dec 14;408(6814):796–815. doi: 10.1038/35048692. [DOI] [PubMed] [Google Scholar]
  2. Cubas P., Vincent C., Coen E. An epigenetic mutation responsible for natural variation in floral symmetry. Nature. 1999 Sep 9;401(6749):157–161. doi: 10.1038/43657. [DOI] [PubMed] [Google Scholar]
  3. Doebley J., Lukens L. Transcriptional regulators and the evolution of plant form. Plant Cell. 1998 Jul;10(7):1075–1082. doi: 10.1105/tpc.10.7.1075. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Doebley J., Stec A., Hubbard L. The evolution of apical dominance in maize. Nature. 1997 Apr 3;386(6624):485–488. doi: 10.1038/386485a0. [DOI] [PubMed] [Google Scholar]
  5. Glover B. J., Perez-Rodriguez M., Martin C. Development of several epidermal cell types can be specified by the same MYB-related plant transcription factor. Development. 1998 Sep;125(17):3497–3508. doi: 10.1242/dev.125.17.3497. [DOI] [PubMed] [Google Scholar]
  6. Grotewold E., Chamberlin M., Snook M., Siame B., Butler L., Swenson J., Maddock S., St Clair G., Bowen B. Engineering secondary metabolism in maize cells by ectopic expression of transcription factors. Plant Cell. 1998 May;10(5):721–740. [PMC free article] [PubMed] [Google Scholar]
  7. Jaglo-Ottosen K. R., Gilmour S. J., Zarka D. G., Schabenberger O., Thomashow M. F. Arabidopsis CBF1 overexpression induces COR genes and enhances freezing tolerance. Science. 1998 Apr 3;280(5360):104–106. doi: 10.1126/science.280.5360.104. [DOI] [PubMed] [Google Scholar]
  8. Jin H., Cominelli E., Bailey P., Parr A., Mehrtens F., Jones J., Tonelli C., Weisshaar B., Martin C. Transcriptional repression by AtMYB4 controls production of UV-protecting sunscreens in Arabidopsis. EMBO J. 2000 Nov 15;19(22):6150–6161. doi: 10.1093/emboj/19.22.6150. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Kempin S. A., Savidge B., Yanofsky M. F. Molecular basis of the cauliflower phenotype in Arabidopsis. Science. 1995 Jan 27;267(5197):522–525. doi: 10.1126/science.7824951. [DOI] [PubMed] [Google Scholar]
  10. Kirschner M., Gerhart J. Evolvability. Proc Natl Acad Sci U S A. 1998 Jul 21;95(15):8420–8427. doi: 10.1073/pnas.95.15.8420. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Kranz H. D., Denekamp M., Greco R., Jin H., Leyva A., Meissner R. C., Petroni K., Urzainqui A., Bevan M., Martin C. Towards functional characterisation of the members of the R2R3-MYB gene family from Arabidopsis thaliana. Plant J. 1998 Oct;16(2):263–276. doi: 10.1046/j.1365-313x.1998.00278.x. [DOI] [PubMed] [Google Scholar]
  12. Lee M. M., Schiefelbein J. Developmentally distinct MYB genes encode functionally equivalent proteins in Arabidopsis. Development. 2001 May;128(9):1539–1546. doi: 10.1242/dev.128.9.1539. [DOI] [PubMed] [Google Scholar]
  13. Liu Q., Kasuga M., Sakuma Y., Abe H., Miura S., Yamaguchi-Shinozaki K., Shinozaki K. Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought- and low-temperature-responsive gene expression, respectively, in Arabidopsis. Plant Cell. 1998 Aug;10(8):1391–1406. doi: 10.1105/tpc.10.8.1391. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Lloyd A. M., Walbot V., Davis R. W. Arabidopsis and Nicotiana anthocyanin production activated by maize regulators R and C1. Science. 1992 Dec 11;258(5089):1773–1775. doi: 10.1126/science.1465611. [DOI] [PubMed] [Google Scholar]
  15. McMullen M. D., Byrne P. F., Snook M. E., Wiseman B. R., Lee E. A., Widstrom N. W., Coe E. H. Quantitative trait loci and metabolic pathways. Proc Natl Acad Sci U S A. 1998 Mar 3;95(5):1996–2000. doi: 10.1073/pnas.95.5.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Michaels S. D., Amasino R. M. FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell. 1999 May;11(5):949–956. doi: 10.1105/tpc.11.5.949. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Payne T., Clement J., Arnold D., Lloyd A. Heterologous myb genes distinct from GL1 enhance trichome production when overexpressed in Nicotiana tabacum. Development. 1999 Feb;126(4):671–682. doi: 10.1242/dev.126.4.671. [DOI] [PubMed] [Google Scholar]
  18. Pelaz S., Ditta G. S., Baumann E., Wisman E., Yanofsky M. F. B and C floral organ identity functions require SEPALLATA MADS-box genes. Nature. 2000 May 11;405(6783):200–203. doi: 10.1038/35012103. [DOI] [PubMed] [Google Scholar]
  19. Peng J., Carol P., Richards D. E., King K. E., Cowling R. J., Murphy G. P., Harberd N. P. The Arabidopsis GAI gene defines a signaling pathway that negatively regulates gibberellin responses. Genes Dev. 1997 Dec 1;11(23):3194–3205. doi: 10.1101/gad.11.23.3194. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Peng J., Richards D. E., Hartley N. M., Murphy G. P., Devos K. M., Flintham J. E., Beales J., Fish L. J., Worland A. J., Pelica F. 'Green revolution' genes encode mutant gibberellin response modulators. Nature. 1999 Jul 15;400(6741):256–261. doi: 10.1038/22307. [DOI] [PubMed] [Google Scholar]
  21. Peña L., Martín-Trillo M., Juárez J., Pina J. A., Navarro L., Martínez-Zapater J. M. Constitutive expression of Arabidopsis LEAFY or APETALA1 genes in citrus reduces their generation time. Nat Biotechnol. 2001 Mar;19(3):263–267. doi: 10.1038/85719. [DOI] [PubMed] [Google Scholar]
  22. Riechmann J. L., Heard J., Martin G., Reuber L., Jiang C., Keddie J., Adam L., Pineda O., Ratcliffe O. J., Samaha R. R. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science. 2000 Dec 15;290(5499):2105–2110. doi: 10.1126/science.290.5499.2105. [DOI] [PubMed] [Google Scholar]
  23. Sablowski R. W., Meyerowitz E. M. A homolog of NO APICAL MERISTEM is an immediate target of the floral homeotic genes APETALA3/PISTILLATA. Cell. 1998 Jan 9;92(1):93–103. doi: 10.1016/s0092-8674(00)80902-2. [DOI] [PubMed] [Google Scholar]
  24. Simon R., Igeño M. I., Coupland G. Activation of floral meristem identity genes in Arabidopsis. Nature. 1996 Nov 7;384(6604):59–62. doi: 10.1038/384059a0. [DOI] [PubMed] [Google Scholar]
  25. Singh K. B. Transcriptional regulation in plants: the importance of combinatorial control. Plant Physiol. 1998 Dec;118(4):1111–1120. doi: 10.1104/pp.118.4.1111. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Stracke R., Werber M., Weisshaar B. The R2R3-MYB gene family in Arabidopsis thaliana. Curr Opin Plant Biol. 2001 Oct;4(5):447–456. doi: 10.1016/s1369-5266(00)00199-0. [DOI] [PubMed] [Google Scholar]
  27. Tamagnone L, Merida A, Parr A, Mackay S, Culianez-Macia FA, Roberts K, Martin C. The AmMYB308 and AmMYB330 transcription factors from antirrhinum regulate phenylpropanoid and lignin biosynthesis in transgenic tobacco . Plant Cell. 1998 Feb;10(2):135–154. doi: 10.1105/tpc.10.2.135. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Thornsberry J. M., Goodman M. M., Doebley J., Kresovich S., Nielsen D., Buckler E. S., 4th Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet. 2001 Jul;28(3):286–289. doi: 10.1038/90135. [DOI] [PubMed] [Google Scholar]
  29. Weigel D., Nilsson O. A developmental switch sufficient for flower initiation in diverse plants. Nature. 1995 Oct 12;377(6549):495–500. doi: 10.1038/377495a0. [DOI] [PubMed] [Google Scholar]
  30. Yano M., Katayose Y., Ashikari M., Yamanouchi U., Monna L., Fuse T., Baba T., Yamamoto K., Umehara Y., Nagamura Y. Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell. 2000 Dec;12(12):2473–2484. doi: 10.1105/tpc.12.12.2473. [DOI] [PMC free article] [PubMed] [Google Scholar]

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