Bioinformatic landscapes for plant transcription factor system research

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• 作者：Yijun Wang ; Wenjie Lu ; Dexiang Deng
• 关键词：Plant transcription factors ; Bioinformatics ; ; omics ; Systems biology
• 刊名：Planta
• 出版年：2016
• 出版时间：February 2016
• 年：2016
• 卷：243
• 期：2
• 页码：297-304
• 全文大小：580 KB
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• 作者单位：Yijun Wang (1)
  Wenjie Lu (1)
  Dexiang Deng (1)
  
  1. 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
  
• 刊物主题：Plant Sciences; Agriculture; Ecology; Forestry;
• 出版者：Springer Berlin Heidelberg
• ISSN：1432-2048

文摘

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.