Abstract
Main conclusion
Diverse bioinformatic resources have been developed for plant transcription factor (TF) research. This review presents the bioinformatic resources and methodologies for the elucidation of plant TF-mediated biological events. Such information is helpful to dissect the transcriptional regulatory systems in the three reference plants Arabidopsis , rice, and maize and translation to other plants.
Transcription factors (TFs) orchestrate diverse biological programs by the modulation of spatiotemporal patterns of gene expression via binding cis-regulatory elements. Advanced sequencing platforms accompanied by emerging bioinformatic tools revolutionize the scope and extent of TF research. The system-level integration of bioinformatic resources is beneficial to the decoding of TF-involved networks. Herein, we first briefly introduce general and specialized databases for TF research in three reference plants Arabidopsis, rice, and maize. Then, as proof of concept, we identified and characterized heat shock transcription factor (HSF) members through the TF databases. Finally, we present how the integration of bioinformatic resources at -omics layers can aid the dissection of TF-mediated pathways. We also suggest ways forward to improve the bioinformatic resources of plant TFs. Leveraging these bioinformatic resources and methodologies opens new avenues for the elucidation of transcriptional regulatory systems in the three model systems and translation to other plants.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Aoki K, Ogata Y, Shibata D (2007) Approaches for extracting practical information from gene co-expression networks in plant biology. Plant Cell Physiol 48:381–390
Bülow L, Brill Y, Hehl R (2010) AthaMap-assisted transcription factor target gene identification in Arabidopsis thaliana. Database 2010:baq034
Carretero-Paulet L, Librado P, Chang TH, Ibarra-Laclette E, Herrera-Estrella L, Rozas J et al (2015) High gene family turnover rates and gene space adaptation in the compact genome of the carnivorous plant Utricularia gibba. Mol Biol Evol 32:1284–1295
Clauw P, Coppens F, De Beuf K, Dhondt S, Van Daele T, Maleux K et al (2015) Leaf responses to mild drought stress in natural variants of Arabidopsis. Plant Physiol 167:800–816
Dash S, Van Hemert J, Hong L, Wise RP, Dickerson JA (2012) PLEXdb: gene expression resources for plants and plant pathogens. Nucl Acids Res 40:D1194–D1201
De Bodt S, Hollunder J, Nelissen H, Meulemeester N, Inzé D (2012) CORNET 2.0: integrating plant coexpression, protein-protein interactions, regulatory interactions, gene associations and functional annotations. New Phytol 195:707–720
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR et al (2014) Pfam: the protein families database. Nucl Acids Res 42:D222–D230
Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R (2014) DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci 111:2367–2372
Godoy M, Franco-Zorrilla JM, Pérez-Pérez J, Oliveros JC, Lorenzo O, Solano R (2011) Improved protein-binding microarrays for the identification of DNA-binding specificities of transcription factors. Plant J 66:700–711
Goff SA, Vaughn M, McKay S, Lyons E, Stapleton AE, Gessler D et al (2011) The iPlant collaborative: cyberinfrastructure for plant biology. Front Plant Sci 2:34
Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J et al (2012) Phytozome: a comparative platform for green plant genomics. Nucl Acids Res 40:D1178–D1186
Heyndrickx KS, Van de Velde J, Wang C, Weigel D, Vandepoele K (2014) A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana. Plant Cell 26:3894–3910
Hieno A, Naznin HA, Hyakumachi M, Sakurai T, Tokizawa M, Koyama H et al (2014) ppdb: plant promoter database version 3.0. Nucl Acids Res 42:D1188–D1192
Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucl Acids Res 27:297–300
Jin J, Zhang H, Kong L, Gao G, Luo J (2014) PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucl Acids Res 42:D1182–D1187
Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C et al (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics 30:1236–1240
Lang D, Weiche B, Timmerhaus G, Richardt S, Riaño-Pachón DM, Corrêa LG et al (2010) Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol 2:488–503
Lee I, Seo YS, Coltrane D, Hwang S, Oh T, Marcotte EM et al (2011) Genetic dissection of the biotic stress response using a genome-scale gene network for rice. Proc Natl Acad Sci 108:18548–18553
Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y et al (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucl Acids Res 30:325–327
Lin JJ, Yu CP, Chang YM, Chen SC, Li WH (2014) Maize and millet transcription factors annotated using comparative genomic and transcriptomic data. BMC Genom 15:818
Lind C, Dreyer I, López-Sanjurjo EJ, von Meyer K, Ishizaki K, Kohchi T et al (2015) Stomatal guard cells co-opted an ancient ABA-dependent desiccation survival system to regulate stomatal closure. Curr Biol 25:928–935
Marín-de la Rosa N, Sotillo B, Miskolczi P, Gibbs DJ, Vicente J, Carbonero P et al (2010) Large-scale identification of gibberellin-related transcription factors defines group VII ethylene response factors as functional della partners. Plant Physiol 166:1022–1032
Martinez M (2011) Plant protein-coding gene families: emerging bioinformatics approaches. Trends Plant Sci 16:558–567
Mochida K, Yoshida T, Sakurai T, Yamaguchi-Shinozaki K, Shinozaki K, Tran LS (2011) In silico analysis of transcription factor repertoires and prediction of stress-responsive transcription factors from six major Gramineae plants. DNA Res 18:321–332
Monaco MK, Sen TZ, Dharmawardhana PD, Ren L, Schaeffer M, Naithani S et al (2013) Maize metabolic network construction and transcriptome analysis. Plant Genome 6:1–12
Obayashi T, Okamura Y, Ito S, Tadaka S, Aoki Y, Shirota M et al (2014) ATTED-II in 2014: evaluation of gene coexpression in agriculturally important plants. Plant Cell Physiol 55:e6
Pérez-Rodríguez P, Riaño-Pachón DM, Corrêa LG, Rensing SA, Kersten B, Mueller-Roeber B (2010) PlnTFDB: updated content and new features of the plant transcription factor database. Nucl Acids Res 38:D822–D827
Phillips T, Hoopes L (2008) Transcription factors and transcriptional control in eukaryotic cells. Nat Educ 1:119
Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, Valen E et al (2010) JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucl Acids Res 38:D105–D110
Priya P, Jain M (2013) RiceSRTFDB: a database of rice transcription factors containing comprehensive expression, cis-regulatory element and mutant information to facilitate gene function analysis. Database 2013:bat027
Proost S, Van Bel M, Vaneechoutte D, Van de Peer Y, Inzé D, Mueller-Roeber B et al (2015) PLAZA 3.0: an access point for plant comparative genomics. Nucl Acids Res 43:D974–D981
Rice Full-Length cDNA Consortium et al (2003) Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301:376–379
Riechmann JL, Heard J, Martin G, Reuber L, Jiang C, Keddie J et al (2000) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290:2105–2110
Rouard M, Guignon V, Aluome C, Laporte MA, Droc G, Walde C et al (2011) GreenPhylDB v2.0: comparative and functional genomics in plants. Nucl Acids Res 39:D1095–D1102
Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183
Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J et al (2015) STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucl Acids Res 43:D447–D452
Vogel JT, Zarka DG, Van Buskirk HA, Fowler SG, Thomashow MF (2005) Roles of the CBF2 and ZAT12 transcription factors in configuring the low temperature transcriptome of Arabidopsis. Plant J 41:195–211
Wang Y, Deng D, Zhang R, Wang S, Bian Y, Yin Z (2012) Systematic analysis of plant-specific B3 domain-containing proteins based on the genome resources of 11 sequenced species. Mol Biol Rep 39:6267–6282
Weirauch MT, Yang A, Albu M, Cote AG, Montenegro-Montero A, Drewe P et al (2014) Determination and inference of eukaryotic transcription factor sequence specificity. Cell 158:1431–1443
Wingender E (1988) Compilation of transcription regulating proteins. Nucl Acids Res 16:1879–1902
Wingender E, Chen X, Fricke E, Geffers R, Hehl R, Liebich I et al (2001) The TRANSFAC system on gene expression regulation. Nucl Acids Res 29:281–283
Yamasaki K, Kigawa T, Seki M, Shinozaki K, Yokoyama S (2013) DNA-binding domains of plant-specific transcription factors: structure, function, and evolution. Trends Plant Sci 18:267–276
Yang JH, Li JH, Jiang S, Zhou H, Qu LH (2013) ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. Nucl Acids Res 41:D177–D187
Yilmaz A, Nishiyama MY Jr, Fuentes BG, Souza GM, Janies D, Gray J et al (2009) GRASSIUS: a platform for comparative regulatory genomics across the grasses. Plant Physiol 149:171–180
Yilmaz A, Mejia-Guerra MK, Kurz K, Liang X, Welch L, Grotewold E (2011) AGRIS: the Arabidopsis gene regulatory information server, an update. Nucl Acids Res 39:D1118–D1122
Acknowledgments
We apologize for not being able to cite many relevant original papers owing to space limitations. This work was supported by the National Natural Science Foundation of China (31201213 and 31571671), the Priority Academic Program Development of Jiangsu Higher Education Institutions, and the Open Project Program of Shanghai Key Laboratory of Bio-Energy Crops, Shanghai University (201302).
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Wang, Y., Lu, W. & Deng, D. Bioinformatic landscapes for plant transcription factor system research. Planta 243, 297–304 (2016). https://doi.org/10.1007/s00425-015-2453-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00425-015-2453-7