ArticleBMC plant biology2012
Bioinformatic cis-element analyses performed in Arabidopsis and rice disclose bZIP- and MYB-related binding sites as potential AuxRE-coupling elements in auxin-mediated transcription.
Article in BMC plant biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed, 102 citations in OpenAlex.
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- Characterization of Transcription Regulatory Domains of OsMADS29: Identification of Proximal Auxin-Responsive Domains and a Strong Distal Negative Element.Frontiers in plant science · 2022Article
- Genome-wide identification of auxin response factor (Physiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
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- Expression Analysis of Key Auxin Biosynthesis, Transport, and Metabolism Genes ofPlants (Basel, Switzerland) · 2020Article
- Identification of theInternational journal of molecular sciences · 2020Article
- The bZIP53-IAA4 module inhibits adventitious root development in Populus.Journal of experimental botany · 2020Article
- The HD-ZIP II Transcription Factors Regulate Plant Architecture through the Auxin Pathway.International journal of molecular sciences · 2020Article
- Specificity in Auxin Responses Is Not Explained by the Promoter Preferences of Activator ARFs.Plant physiology · 2020Article
- An inferred fitness consequence map of the rice genome.Nature plants · 2020Article
- The specific MYB binding sites bound by TaMYB in the GAPCp2/3 promoters are involved in the drought stress response in wheat.BMC plant biology · 2019Article
- Shared cis-regulatory architecture identified across defense response genes is associated with broad-spectrum quantitative resistance in rice.Scientific reports · 2019Article
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6 authors at 2 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundIn higher plants, a diverse array of developmental and growth-related processes is regulated by the plant hormone auxin. Recent publications have proposed that besides the well-characterized Auxin Response Factors (ARFs) that bind Auxin Response Elements (AuxREs), also members of the bZIP- and MYB-transcription factor (TF) families participate in transcriptional control of auxin-regulated genes via bZIP Response Elements (ZREs) or Myb Response Elements (MREs), respectively.
resultsApplying a novel bioinformatic algorithm, we demonstrate on a genome-wide scale that singular motifs or composite modules of AuxREs, ZREs, MREs but also of MYC2 related elements are significantly enriched in promoters of auxin-inducible genes. Despite considerable, species-specific differences in the genome structure in terms of the GC content, this enrichment is generally conserved in dicot (Arabidopsis thaliana) and monocot (Oryza sativa) model plants. Moreover, an enrichment of defined composite modules has been observed in selected auxin-related gene families. Consistently, a bipartite module, which encompasses a bZIP-associated G-box Related Element (GRE) and an AuxRE motif, has been found to be highly enriched. Making use of transient reporter studies in protoplasts, these findings were experimentally confirmed, demonstrating that GREs functionally interact with AuxREs in regulating auxin-mediated transcription.
conclusionsUsing genome-wide bioinformatic analyses, evolutionary conserved motifs have been defined which potentially function as AuxRE-dependent coupling elements to establish auxin-specific expression patterns. Based on these findings, experimental approaches can be designed to broaden our understanding of combinatorial, auxin-controlled gene regulation.
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