Abstract:
: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.
journal_name
Plant Physioljournal_title
Plant physiologyauthors
Ezer D,Shepherd SJK,Brestovitsky A,Dickinson P,Cortijo S,Charoensawan V,Box MS,Biswas S,Jaeger KE,Wigge PAdoi
10.1104/pp.17.01086subject
Has Abstractpub_date
2017-10-01 00:00:00pages
628-640issue
2eissn
0032-0889issn
1532-2548pii
pp.17.01086journal_volume
175pub_type
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