The G-Box Transcriptional Regulatory Code in Arabidopsis1[OPEN]

DNA-binding and gene expression data predict which bHLH or bZIP transcription factors are likely regulators of genes near perfect G-box (CACGTG) motifs. Plants have significantly more transcription factor ( TF ) families than animals and fungi, and plant TF families tend to contain more genes; these...

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Published inPlant physiology (Bethesda) Vol. 175; no. 2; pp. 628 - 640
Main Authors Ezer, Daphne, Shepherd, Samuel J.K., Brestovitsky, Anna, Dickinson, Patrick, Cortijo, Sandra, Charoensawan, Varodom, Box, Mathew S., Biswas, Surojit, Jaeger, Katja E., Wigge, Philip A.
Format Journal Article
LanguageEnglish
Published American Society of Plant Biologists 01.09.2017
Subjects
Breakthrough Technologies
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Summary:DNA-binding and gene expression data predict which bHLH or bZIP transcription factors are likely regulators of genes near perfect G-box (CACGTG) motifs. 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.
Bibliography:The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Philip A. Wigge (philip.wigge@slcu.cam.ac.uk).
www.plantphysiol.org/cgi/doi/10.1104/pp.17.01086
Current address: Harvard Medical School, Division of Medical Sciences, Boston, MA 02115.
D.E. conceived of the idea of the project, did most of the analysis, wrote the software, and wrote most of the article; S.J.K.S. assisted with the analysis for Figure 2; A.B. designed and conducted the MNase-seq experiment; A.B., P.D., S.C., V.C., and M.S.B. designed and conducted RNA-seq experiments; S.C., V.C., and S.B. helped map the RNA-seq data; K.E.J. conducted the ChIP-seq experiments; P.A.W. supervised and contributed to writing the article.
ISSN:0032-0889
1532-2548
DOI:10.1104/pp.17.01086