title: Bioinformatic landscapes for plant transcription factor system research.
abstract: 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.
authors.affiliation: Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China. wyj@yzu.edu.cn.
authors.forename: Yijun
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
authors.forename: Wenjie
authors.initials: W
authors.lastname: Lu
authors.affiliation: Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
authors.forename: Dexiang
authors.initials: D
authors.lastname: Deng
mesh_terms: D019295:Computational Biology; D030541:Databases, Genetic; D018506:Gene Expression Regulation, Plant; D010940:Plant Proteins / Q000737:chemistry / Q000378:metabolism / Q000502:physiology*; D010944:Plants / Q000235:genetics*; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism / Q000502:physiology*; D059467:Transcriptome
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors
keywords: -omics; Bioinformatics; Plant transcription factors; Systems biology