AthaMap, a database for the identification of combinatorial elements by colocalization analysis of transcription factor binding sites

Pflanzen können auf Veränderungen der Umweltbedingungen durch eine Vielzahl von Anpassungen reagieren. In vielen Fällen wird diese Anpassung durch ein verändertes Muster der Genexpression hervorgerufen, an dessen Anfang die transkriptionellen Regulatoren stehen, die Transkriptionsfaktoren (TFs). Die Identifizierung von Transkriptionsfaktorbindungsstellen (TFBS) in regulatorischen Bereichen ermöglicht es, Vorhersagen über die potentielle Regulation von Genen zu machen. Die potentiellen TFBS von 36 pflanzlichen TFs wurden durch genomweites Matrizen-Screening in Arabidopsis thaliana identifiziert und in der neu erstellten AthaMap Datenbank annotiert. Insgesamt wurden ca. 7,5 Mio. TFBS sowie ca. 180.000 kombinatorische Elemente annotiert. Für diese Datenbank wurde ein Webinterface implementiert (www.AthaMap.de), das frei zugänglich für alle Benutzer potentielle TFBS und kombinatorische Elemente im Arabidopsis-Genom visualisiert. Basierend auf der Beobachtung daß die TFBS interagierender TFs häufiger colokalisieren als die TFBS nicht interagierender TFs wurde ein Webtool zur Detektion colokalisierender TFBS anhand benutzerdefinierter Parameter implementiert. Um detailliertere Untersuchungen über die Interaktionen des TBP durchführen zu können wurden die putativ funktionellen TATA-Boxen im Arabidopsis-Genom identifziert. Dabei zeigte sich, daß nur ca. ein Drittel aller Arabidopsis-Gene eine TATA-Box besitzt. Durch Colokalisationsanalysen von TATA-Boxen und Bindungsstellen des bZIP-TFs ABF1 wurde ein neues potentielles kombinatorisches Abscisinsäure-Response-Element (ABRE) identifiziert, das aus einer TATA-Box und einer ABF1-Bindungsstelle besteht. Es wurde gezeigt, daß das Auftreten dieses neuen ABREs im Upstreambereich von Genen mit einer ABA-Induzierbarkeit dieser Gene korreliert.Plants can adapt to changing environmental conditions by a variety of adaptive mechanisms. Frequently, adaption is aqquired by changes in the gene expression patterns, which are regulated by transcription factors (TFs). The identification of potential transcription factor binding sites (TFBS) in regulatory regions of genes facilitates the prediction of gene regulation. The potential TFBS of 36 plant transcription factors were identified by genomic matrice screening in Arabidopsis thaliana and subsequently annotated in the newly generated AthaMap database. In all, about 7.5 mio TFBS and about 180.000 combinatorial elements were annotated. For this database, a webinterface was implemented (www.AthaMap.de) which is freely accessible to all users and visualizes potential TFBS and combinatorial elements in the Arabidopsis genome. Based on the observation that TFBS of interacting TFs colocalize more often than the TFBS of non-interacting TFBS, a webtool was generated which detects colocalization of TFBS according to parameters specified by the user. In order to perform specific analysis about TBP-interactions, putatively functional TATA-boxes were identified in the Arabidopsis genome. It was shown that only about a third of all Arabidopsis genes contain TATA-boxes in their promoters. A new potential Abscisin-response-element (ABRE) consisting of a TATA-box and an ABF1-binding site was identified by colocalization analysis of TATA-boxes and ABF1 binding sites. Furthermore, it was shown that the occurrence of this ABRE correlates with ABA-inducibility of the respective genes

AthaMap web tools for database-assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana

The AthaMap database generates a map of cis-regulatory elements for the Arabidopsis thaliana genome. AthaMap contains more than 7.4 × 10(6) putative binding sites for 36 transcription factors (TFs) from 16 different TF families. A newly implemented functionality allows the display of subsets of higher conserved transcription factor binding sites (TFBSs). Furthermore, a web tool was developed that permits a user-defined search for co-localizing cis-regulatory elements. The user can specify individually the level of conservation for each TFBS and a spacer range between them. This web tool was employed for the identification of co-localizing sites of known interacting TFs and TFs containing two DNA-binding domains. More than 1.8 × 10(5) combinatorial elements were annotated in the AthaMap database. These elements can also be used to identify more complex co-localizing elements consisting of up to four TFBSs. The AthaMap database and the connected web tools are a valuable resource for the analysis and the prediction of gene expression regulation at

Characterization of the actin binding properties of the vasodilator-stimulated phosphoprotein VASP

AbstractThe vasodilator-stimulated phosphoprotein (VASP) colocalizes with the ends of stress fibers in cell-matrix and cell-cell contacts. We report here that bacterially expressed murine VASP directly interacts with skeletal muscle actin in several test systems including cosedimentation, viscometry and polymerization assays. It nucleates actin polymerization and tightly bundles actin filaments. The interaction with actin is salt-sensitive, indicating that the complex formation is primarily based on electrostatic interactions. Actin binding is confined to the C-terminal domain of VASP (EVH2). This domain, when expressed as a fusion protein with EGFP, associates with stress fibers in transiently transfected cells

AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome

Gene expression is controlled mainly by the binding of transcription factors to regulatory sequences. To generate a genomic map for regulatory sequences, the Arabidopsis thaliana genome was screened for putative transcription factor binding sites. Using publicly available data from the TRANSFAC database and from publications, alignment matrices for 23 transcription factors of 13 different factor families were used with the pattern search program Patser to determine the genomic positions of more than 2.4 × 10(6) putative binding sites. Due to the dense clustering of genes and the observation that regulatory sequences are not restricted to upstream regions, the prediction of binding sites was performed for the whole genome. The genomic positions and the underlying data were imported into the newly developed AthaMap database. This data can be accessed by positional information or the Arabidopsis Genome Initiative identification number. Putative binding sites are displayed in the defined region. Data on the matrices used and on the thresholds applied in these screens are given in the database. Considering the high density of sites it will be a valuable resource for generating models on gene expression regulation. The data are available at http://www.athamap.de

IOS Press AthaMap: From in silico Datato Real Transcription Factor Binding Sites

ABSTRACT: AthaMap generates a map for cis-regulatory sequences for the whole Arabidopsis thaliana genome. AthaMap was initially developed by matrix-based detection of putative transcription factor binding sites (TFBS) mostly determined from random binding site selection experiments. Now, also experimentally verified TFBS have been included for 48 different Arabidopsis thaliana transcription factors (TF). Based on these sequences, 89,416 very similar putative TFBS were determined within the genome of A. thaliana and annotated to AthaMap. Matrix- and single sequence-based binding sites can be included in colocalization analysis for the identification of combinatorial cis-regulatory elements. As an example, putative target genes of the WRKY18 transcription factor that is involved in plant-pathogen interaction were determined. New functions of AthaMap include descriptions for all annotated Arabidopsis thaliana genes and direct links to TAIR, TIGR and MIPS. Transcription factors used in the binding site determination are linked to TAIR and TRANSFAC databases. AthaMap is freely available a