Open Access Research article

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

Kenneth W Berendzen1, Christoph Weiste2, Dierk Wanke1, Joachim Kilian1, Klaus Harter1* and Wolfgang Dröge-Laser2*

Author Affiliations

1 Zentrum für Molekularbiologie der Pflanzen, Pflanzenphysiologie, Universität Tübingen, Auf der Morgenstelle 1, 72076, Tübingen, Germany

2 Julius-von-Sachs-Institut, Pharmazeutische Biologie, Universität Würzburg, Julius-von-Sachs-Platz 2, 97082, Würzburg, Germany

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BMC Plant Biology 2012, 12:125  doi:10.1186/1471-2229-12-125

Published: 1 August 2012

Additional files

Additional file 1:

Expression-profiles of auxin-regulated genes from A. thaliana. Number of auxin-regulated genes determined to be regulated and being significantly (α ≤ 0.05), 2-fold up- or down- regulated compared to the control for each time point. Non-redundant genes identified on ATH1 chip ('On Chip') and the number of genes for which a corresponding promoter could be found ('With Prom.') are given. Expression profiles of these genes are shown. Microarray analysis is explained in the Methods section.

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Additional file 2:

Auxin-regulated genes from A. thalianaandO. sativa. List of auxin-regulated genes for each time point ordered in up- and down-regulation categories. Fold induction, Affymetrix identifiers, Locus identifiers and gene descriptions are provided.

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Additional file 3:

Extended occurrence lists from A.thalianaandO.sativa. Extended occurrence lists of enriched motifs and modules from auxin inducible promoters from Arabidopsis, rice and selected auxin-related gene families. Enrichment of cis-elements in promoters was determined by parameter I, whereas asterisks indicate an enrichment with respect to parameter II. The number of analysed promoters as well as that of promoters containing at least one of the presented motifs or modules is given in parentheses. Presented modules (bipartite, tripartite) exhibit a variable, but maximal spacing of 100 bps between each embedded motif. Sequences and abbreviations of cis-elements are given in Table 1.

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Additional file 4:

Expression-profiles of auxin-regulated genes from O. sativa. Number of auxin-regulated probe sets ('Probes') determined to be regulated and being significantly (α ≤ 0.05), 2-fold up- or down-regulated compared to the control. From those probes, a sub-set could be mapped to a set of non-redundant genes ('OsGI') and for most of them the corresponding promoters could be found ('Promoter'). Expression profiles of these probes are shown. Microarray analysis is explained in the Methods section.

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Additional file 5:

Auxin-regulated gene family members from A. thaliana. Presented are gene members of auxin-related gene families used in this work, with identifiers and gene descriptions extracted from the TAIR9 functional descriptions and current gene family classifications [36,69,70].

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