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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #345484

Research Project: Genetic and Genomic Basis of Vegetable and Fruit Biology, Quality and Nutrient Content

Location: Plant, Soil and Nutrition Research

Title: iTAK: A program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators and protein kinases

Author
item Zheng, Yi - Boyce Thompson Institute
item Jiao, Chen - Boyce Thompson Institute
item Honghe, Sun - Boyce Thompson Institute
item Rosli, Hernan - Boyce Thompson Institute
item Pombo, Marina - Boyce Thompson Institute
item Martin, Gregory - Boyce Thompson Institute
item Giovannoni, James
item Fei, Zhangjun - Boyce Thompson Institute

Submitted to: Molecular Plant
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/28/2016
Publication Date: 12/5/2016
Citation: Zheng, Y., Jiao, C., Honghe, S., Rosli, H., Pombo, M., Martin, G., Giovannoni, J.J., Fei, Z. 2016. iTAK: A program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators and protein kinases. Molecular Plant. 9:1667-1670.

Interpretive Summary: Transcription factors (TFs) and Transcriptional regulators (TRs) are central in regulating genes and bringing about phenotypes related to crop quality and performance. We have derived a set of consensus domain assignment rules for accurate identification and classification of plant TFs and TRs to facilitate their study and eventual use in crop improvement. We have developed a novel bioinformatics tool, iTAK, to facilitate genome-wide identification and classification of plant TFs and TRs, and a comprehensive database for these regulatory proteins from sequenced plant species. These provide valuable tools and resources for the research community to study transcriptional regulations and signaling networks in plants and to eventually take this knowledge forward to crop breeding and improvement.

Technical Abstract: Transcription factors (TFs) are proteins that regulate the expression of target genes by binding to specific elements in their regulatory regions. Transcriptional regulators (TRs) also regulate the expression of target genes; however, they operate indirectly via interaction with the basal transcription apparatus (e.g., TFs), or by altering the accessibility of DNA to TFs via chromatin remodeling. Another type of regulatory proteins, protein kinases (PKs), function in signal transduction pathways and alter the activity of target proteins by phosphorylating them. These three important classes of regulatory proteins have been associated with numerous aspects of plant growth and development, and response to environmental stress. Effective and accurate identification and classification of these genes is important for understanding their evolution, biological functions, and regulatory networks. Currently, more than 100 plant genomes have been sequenced and regulatory proteins have been systematically identified from several of these plant genomes. Databases presenting these regulatory proteins, especially TFs, have been developed. However, annotations of TF/TR families and the associated classification rules have been inconsistent among different studies. In this study, we systemically compared TF/TR classification rules used in different databases, and derived a set of consensus rules based on the available literature for accurate plant TF/TR identification and classification.