Bioinformatic <it>cis</it>-element analyses performed in <it>Arabidopsis</it> and rice disclose bZIP- and MYB-related binding sites as potential AuxRE-coupling elements in auxin-mediated transcription

<p>Abstract</p> <p>Background</p> <p>In 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 Au...

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Main Authors: Berendzen Kenneth W, Weiste Christoph, Wanke Dierk, Kilian Joachim, Harter Klaus, Dröge-Laser Wolfgang
Format: Article
Language:English
Published: BMC 2012-08-01
Series:BMC Plant Biology
Subjects:
Online Access:http://www.biomedcentral.com/1471-2229/12/125
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author Berendzen Kenneth W
Weiste Christoph
Wanke Dierk
Kilian Joachim
Harter Klaus
Dröge-Laser Wolfgang
author_facet Berendzen Kenneth W
Weiste Christoph
Wanke Dierk
Kilian Joachim
Harter Klaus
Dröge-Laser Wolfgang
author_sort Berendzen Kenneth W
collection DOAJ
description <p>Abstract</p> <p>Background</p> <p>In 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.</p> <p>Results</p> <p>Applying 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 (<it>Arabidopsis thaliana</it>) and monocot (<it>Oryza sativa</it>) 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.</p> <p>Conclusions</p> <p>Using 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.</p>
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spelling doaj.art-5a43fe2f5e8143dd87d8260a0473a8942022-12-21T21:21:35ZengBMCBMC Plant Biology1471-22292012-08-0112112510.1186/1471-2229-12-125Bioinformatic <it>cis</it>-element analyses performed in <it>Arabidopsis</it> and rice disclose bZIP- and MYB-related binding sites as potential AuxRE-coupling elements in auxin-mediated transcriptionBerendzen Kenneth WWeiste ChristophWanke DierkKilian JoachimHarter KlausDröge-Laser Wolfgang<p>Abstract</p> <p>Background</p> <p>In 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.</p> <p>Results</p> <p>Applying 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 (<it>Arabidopsis thaliana</it>) and monocot (<it>Oryza sativa</it>) 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.</p> <p>Conclusions</p> <p>Using 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.</p>http://www.biomedcentral.com/1471-2229/12/125<it>Cis</it>-elements<it>cis</it>-element modulesAuxin-regulated transcriptionAuxREbZIPMYBMYC
spellingShingle Berendzen Kenneth W
Weiste Christoph
Wanke Dierk
Kilian Joachim
Harter Klaus
Dröge-Laser Wolfgang
Bioinformatic <it>cis</it>-element analyses performed in <it>Arabidopsis</it> and rice disclose bZIP- and MYB-related binding sites as potential AuxRE-coupling elements in auxin-mediated transcription
BMC Plant Biology
<it>Cis</it>-elements
<it>cis</it>-element modules
Auxin-regulated transcription
AuxRE
bZIP
MYB
MYC
title Bioinformatic <it>cis</it>-element analyses performed in <it>Arabidopsis</it> and rice disclose bZIP- and MYB-related binding sites as potential AuxRE-coupling elements in auxin-mediated transcription
title_full Bioinformatic <it>cis</it>-element analyses performed in <it>Arabidopsis</it> and rice disclose bZIP- and MYB-related binding sites as potential AuxRE-coupling elements in auxin-mediated transcription
title_fullStr Bioinformatic <it>cis</it>-element analyses performed in <it>Arabidopsis</it> and rice disclose bZIP- and MYB-related binding sites as potential AuxRE-coupling elements in auxin-mediated transcription
title_full_unstemmed Bioinformatic <it>cis</it>-element analyses performed in <it>Arabidopsis</it> and rice disclose bZIP- and MYB-related binding sites as potential AuxRE-coupling elements in auxin-mediated transcription
title_short Bioinformatic <it>cis</it>-element analyses performed in <it>Arabidopsis</it> and rice disclose bZIP- and MYB-related binding sites as potential AuxRE-coupling elements in auxin-mediated transcription
title_sort bioinformatic it cis it element analyses performed in it arabidopsis it and rice disclose bzip and myb related binding sites as potential auxre coupling elements in auxin mediated transcription
topic <it>Cis</it>-elements
<it>cis</it>-element modules
Auxin-regulated transcription
AuxRE
bZIP
MYB
MYC
url http://www.biomedcentral.com/1471-2229/12/125
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