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|Title:||The G-box transcriptional regulatory code in arabidopsis|
Samuel J.K. Shepherd
Mathew S. Box
Katja E. Jaeger
Philip A. Wigge
University of Cambridge
Harvard Medical School
|Keywords:||Agricultural and Biological Sciences;Biochemistry, Genetics and Molecular Biology|
|Citation:||Plant Physiology. Vol.175, No.2 (2017), 628-640|
|Abstract:||© 2017 American Society of Plant Biologists. All Rights Reserved. Plants have significantly more transcription factor (TF) families than animals and fungi, and plant TF families tend to contain more genes; these expansions are linked to adaptation to environmental stressors. Many TF family members bind to similar or identical sequence motifs, such as G-boxes (CACGTG), so it is difficult to predict regulatory relationships. We determined that the flanking sequences near G-boxes help determine in vitro specificity but that this is insufficient to predict the transcription pattern of genes near G-boxes. Therefore, we constructed a gene regulatory network that identifies the set of bZIPs and bHLHs that are most predictive of the expression of genes downstream of perfect G-boxes. This network accurately predicts transcriptional patterns and reconstructs known regulatory subnetworks. Finally, we present Ara-BOX-cis (araboxcis.org), a Web site that provides interactive visualizations of the G-box regulatory network, a useful resource for generating predictions for gene regulatory relations.|
|Appears in Collections:||Scopus 2016-2017|
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