DNA-binding specificities of plant transcription factors and their potential to define target genes

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 6, 2014, Pages 2367-2372

  Franco Zorrilla, José M ^a   López Vidriero, Irene ^a   Carrasco, José L ^b   Godoy, Marta ^a   Vera, Pablo ^b   Solano, Roberto ^a  

^a CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

^b CSIC   (Spain)

Author keywords

Arabidopsis; Cis element; Coregulation; Regulatory network; Transcriptional regulation

Indexed keywords

ARABIDOPSIS; CIS-ELEMENT; COREGULATION; REGULATORY NETWORK; TRANSCRIPTIONAL REGULATION;

ARABIDOPSIS; BINDING SITES; DNA, PLANT; GENES, PLANT; TRANSCRIPTION FACTORS;

EID: 84893861206     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1316278111     Document Type: Article

References (47)

1. Riechmann JL, et al. (2000) Arabidopsis transcription factors: Genome-wide comparative analysis among eukaryotes. Science 290(5499):2105-2110.
2. Harbison CT, et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431(7004):99-104.
3. Badis G, et al. (2009) Diversity and complexity in DNA recognition by transcription factors. Science 324(5935):1720-1723.
4. Jolma A, et al. (2013) DNA-binding specificities of human transcription factors. Cell 152(1-2):327-339.
5. Tanay A (2006) Extensive low-affinity transcriptional interactions in the yeast genome. Genome Res 16(8):962-972.
6. Li XY, et al. (2008) Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol 6(2):e27.
7. Yant L, et al. (2010) Orchestration of the floral transition and floral development in Arabidopsis by the bifunctional transcription factor APETALA2. Plant Cell 22(7):2156-2170.
8. Hornitschek P, et al. (2012) Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling. Plant J 71(5):699-711.
9. Huang W, et al. (2012) Mapping the core of the Arabidopsis circadian clock defines the network structure of the oscillator. Science 336(6077):75-79.
10. Godoy M, et al. (2011) Improved protein-binding microarrays for the identification of DNA-binding specificities of transcription factors. Plant J 66(4):700-711.
11. Shinozaki K, Yamaguchi-Shinozaki K (2000) Molecular responses to dehydration and low temperature: Differences and cross-talk between two stress signaling pathways. Curr Opin Plant Biol 3(3):217-223.
12. Lohmann JU, et al. (2001) A molecular link between stem cell regulation and floral patterning in Arabidopsis. Cell 105(6):793-803.
13. Lowry JA, Atchley WR (2000) Molecular evolution of the GATA family of transcription factors: Conservation within the DNA-binding domain. J Mol Evol 50(2):103-115.
14. Kosugi S, Ohashi Y (2002) DNA binding and dimerization specificity and potential targets for the TCP protein family. Plant J 30(3):337-348.
15. Viola IL, Reinheimer R, Ripoll R, Manassero NG, Gonzalez DH (2012) Determinants of the DNA binding specificity of class I and class II TCP transcription factors. J Biol Chem 287(1):347-356.
16. Ulmasov T, Hagen G, Guilfoyle TJ (1997) ARF1, a transcription factor that binds to auxin response elements. Science 276(5320):1865-1868.
17. Husbands A, Bell EM, Shuai B, Smith HM, Springer PS (2007) LATERAL ORGAN BOUNDARIES defines a new family of DNA-binding transcription factors and can interact with specific bHLH proteins. Nucleic Acids Res 35(19):6663-6671.
18. Eklund DM, et al. (2010) The Arabidopsis thaliana STYLISH1 protein acts as a transcriptional activator regulating auxin biosynthesis. Plant Cell 22(2):349-363.
19. Wu G, et al. (2008) KANADI1 regulates adaxial-abaxial polarity in Arabidopsis by directly repressing the transcription of ASYMMETRIC LEAVES2. Proc Natl Acad Sci USA 105(42):16392-16397.
20. Jung JH, et al. (2007) The GIGANTEA-regulated microRNA172 mediates photoperiodic flowering independent of CONSTANS in Arabidopsis. Plant Cell 19(9):2736-2748.
21. Kanaya E, Nakajima N, Okada K (2002) Non-sequence-specific DNA binding by the FILAMENTOUS FLOWER protein from Arabidopsis thaliana is reduced by EDTA. J Biol Chem 277(14):11957-11964.
22. Dai M, et al. (2007) The rice YABBY1 gene is involved in the feedback regulation of gibberellin metabolism. Plant Physiol 144(1):121-133.
23. Levy YY, Mesnage S, Mylne JS, Gendall AR, Dean C (2002) Multiple roles of Arabidopsis VRN1 in vernalization and flowering time control. Science 297(5579):243-246.
24. Franco-Zorrilla JM, et al. (2002) AtREM1, a member of a new family of B3 domaincontaining genes, is preferentially expressed in reproductive meristems. Plant Physiol 128(2):418-427.
25. Solano R, Fuertes A, Sánchez-Pulido L, Valencia A, Paz-Ares J (1997) A single residue substitution causes a switch from the dual DNA binding specificity of plant transcription factor MYB.Ph3 to the animal c-MYB specificity. J Biol Chem272(5):2889-2895.
26. Hosoda K, et al. (2002) Molecular structure of the GARP family of plant Myb-related DNA binding motifs of the Arabidopsis response regulators. Plant Cell 14(9):2015-2029.
27. Ohme-Takagi M, Shinshi H (1995) Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element. Plant Cell 7(2):173-182.
28. Jakoby M, et al.; bZIP Research Group (2002) bZIP transcription factors in Arabidopsis. Trends Plant Sci 7(3):106-111.
29. Birkenbihl RP, Jach G, Saedler H, Huijser P (2005) Functional dissection of the plantspecific SBP-domain: Overlap of the DNA-binding and nuclear localization domains. J Mol Biol 352(3):585-596.
30. Fujimoto S, et al. (2004) Identification of a novel plant MAR DNA binding protein localized on chromosomal surfaces. Plant Mol Biol 56(2):225-239.
31. Perisic O, Xiao H, Lis JT (1989) Stable binding of Drosophila heat shock factor to headto-head and tail-to-tail repeats of a conserved 5 bp recognition unit. Cell 59(5): 797-806.
32. Sun S, et al. (2008) TINY, a dehydration-responsive element (DRE)-binding protein-like transcription factor connecting the DRE-and ethylene-responsive element-mediated signaling pathways in Arabidopsis. J Biol Chem 283(10):6261-6271.
33. Yanagisawa S (2004) Dof domain proteins: Plant-specific transcription factors associated with diverse phenomena unique to plants. Plant Cell Physiol 45(4):386-391.
34. Thurman RE, et al. (2012) The accessible chromatin landscape of the human genome. Nature 489(7414):75-82.
35. Neph S, et al. (2012) An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 489(7414):83-90.
36. Bernstein BE, et al.; ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57-74.
37. Zhang W, Zhang T, Wu Y, Jiang J (2012) Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis. Plant Cell 24(7):2719-2731.
38. Green KA, Prigge MJ, Katzman RB, Clark SE (2005) CORONA, a member of the class III homeodomain leucine zipper gene family in Arabidopsis, regulates stem cell specification and organogenesis. Plant Cell 17(3):691-704.
39. Saddic LA, et al. (2006) The LEAFY target LMI1 is a meristem identity regulator and acts together with LEAFY to regulate expression of CAULIFLOWER. Development 133(9):1673-1682.
40. Zhang Y, et al. (2013) A quartet of PIF bHLH factors provides a transcriptionally centered signaling hub that regulates seedling morphogenesis through differential expressionpatterning of shared target genes in Arabidopsis. PLoS Genet 9(1):e1003244.
41. Fernández-Calvo P, et al. (2011) The Arabidopsis bHLH transcription factors MYC3 and MYC4 are targets of JAZ repressors and act additively with MYC2 in the activation of jasmonate responses. Plant Cell 23(2):701-715.
42. Wei GH, et al. (2010) Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. EMBO J 29(13):2147-2160.
43. Gordân R, et al. (2011) Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. Genome Biol 12(12):R125.
44. Hammarström M, Hellgren N, van Den Berg S, Berglund H, Härd T (2002) Rapid screening for improved solubility of small human proteins produced as fusion proteins in Escherichia coli. Protein Sci 11(2):313-321.
45. Berger MF, Bulyk ML (2009) Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nat Protoc 4(3):393-411.
46. Hruz T, et al. (2008) Genevestigator v3: A reference expression database for the metaanalysis of transcriptomes. Adv Bioinforma 2008:420747.
47. Tabas-Madrid D, Nogales-Cadenas R, Pascual-Montano A (2012) GeneCodis3: A nonredundant and modular enrichment analysis tool for functional genomics. Nucleic Acids Res 40(Web Server issue):W478-83.