Internet Resources for Gene Expression Analysis in Arabidopsis thaliana

The number of online databases and web-tools for gene expression analysis in Arabidopsis thaliana has increased tremendously during the last years. These resources permit the database-assisted identification of putative cis-regulatory DNA sequences, their binding proteins, and the determination of common cis-regulatory motifs in coregulated genes. DNA binding proteins may be predicted by the type of cis-regulatory motif. Further questions of combinatorial control based on the interaction of DNA binding proteins and the colocalization of cis-regulatory motifs can be addressed. The database-assisted spatial and temporal expression analysis of DNA binding proteins and their target genes may help to further refine experimental approaches. Signal transduction pathways upstream of regulated genes are not yet fully accessible in databases mainly because they need to be manually annotated. This review focuses on the use of the AthaMap and PathoPlant® databases for gene expression regulation analysis and discusses similar and complementary online databases and web-tools. Online databases are helpful for the development of working hypothesis and for designing subsequent experiments

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

AthaMap web tools for the analysis and identification of co-regulated genes

The AthaMap database generates a map of cis-regulatory elements for the whole Arabidopsis thaliana genome. This database has been extended by new tools to identify common cis-regulatory elements in specific regions of user-provided gene sets. A resulting table displays all cis-regulatory elements annotated in AthaMap including positional information relative to the respective gene. Further tables show overviews with the number of individual transcription factor binding sites (TFBS) present and TFBS common to the whole set of genes. Over represented cis-elements are easily identified. These features were used to detect specific enrichment of drought-responsive elements in cold-induced genes. For identification of co-regulated genes, the output table of the colocalization function was extended to show the closest genes and their relative distances to the colocalizing TFBS. Gene sets determined by this function can be used for a co-regulation analysis in microarray gene expression databases such as Genevestigator or PathoPlant. Additional improvements of AthaMap include display of the gene structure in the sequence window and a significant data increase. AthaMap is freely available at

PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups

<p>Abstract</p> <p>Background</p> <p>The elucidation of transcriptional regulation in plant genes is important area of research for plant scientists, following the mapping of various plant genomes, such as <it>A. thaliana</it>, <it>O. sativa </it>and <it>Z. mays</it>. A variety of bioinformatic servers or databases of plant promoters have been established, although most have been focused only on annotating transcription factor binding sites in a single gene and have neglected some important regulatory elements (tandem repeats and CpG/CpNpG islands) in promoter regions. Additionally, the combinatorial interaction of transcription factors (TFs) is important in regulating the gene group that is associated with the same expression pattern. Therefore, a tool for detecting the co-regulation of transcription factors in a group of gene promoters is required.</p> <p>Results</p> <p>This study develops a database-assisted system, PlantPAN (Plant Promoter Analysis Navigator), for recognizing combinatorial <it>cis</it>-regulatory elements with a distance constraint in sets of plant genes. The system collects the plant transcription factor binding profiles from PLACE, TRANSFAC (public release 7.0), AGRIS, and JASPER databases and allows users to input a group of gene IDs or promoter sequences, enabling the co-occurrence of combinatorial transcription factor binding sites (TFBSs) within a defined distance (20 bp to 200 bp) to be identified. Furthermore, the new resource enables other regulatory features in a plant promoter, such as CpG/CpNpG islands and tandem repeats, to be displayed. The regulatory elements in the conserved regions of the promoters across homologous genes are detected and presented.</p> <p>Conclusion</p> <p>In addition to providing a user-friendly input/output interface, PlantPAN has numerous advantages in the analysis of a plant promoter. Several case studies have established the effectiveness of PlantPAN. This novel analytical resource is now freely available at <url>http://PlantPAN.mbc.nctu.edu.tw</url>.</p

AtPAN: an integrated system for reconstructing transcriptional regulatory networks in Arabidopsis thaliana

<p>Abstract</p> <p>Background</p> <p>Construction of transcriptional regulatory networks (TRNs) is of priority concern in systems biology. Numerous high-throughput approaches, including microarray and next-generation sequencing, are extensively adopted to examine transcriptional expression patterns on the whole-genome scale; those data are helpful in reconstructing TRNs. Identifying transcription factor binding sites (TFBSs) in a gene promoter is the initial step in elucidating the transcriptional regulation mechanism. Since transcription factors usually co-regulate a common group of genes by forming regulatory modules with similar TFBSs. Therefore, the combinatorial interactions of transcription factors must be modeled to reconstruct the gene regulatory networks.</p> <p>Description For systems biology applications, this work develops a novel database called <it>Arabidopsis thaliana </it>Promoter Analysis Net (AtPAN), capable of detecting TFBSs and their corresponding transcription factors (TFs) in a promoter or a set of promoters in <it>Arabidopsis</it>. For further analysis, according to the microarray expression data and literature, the co-expressed TFs and their target genes can be retrieved from AtPAN. Additionally, proteins interacting with the co-expressed TFs are also incorporated to reconstruct co-expressed TRNs. Moreover, combinatorial TFs can be detected by the frequency of TFBSs co-occurrence in a group of gene promoters. In addition, TFBSs in the conserved regions between the two input sequences or homologous genes in <it>Arabidopsis </it>and rice are also provided in AtPAN. The output results also suggest conducting wet experiments in the future.</p> <p>Conclusions</p> <p>The AtPAN, which has a user-friendly input/output interface and provide graphical view of the TRNs. This novel and creative resource is freely available online at <url>http://AtPAN.itps.ncku.edu.tw/</url>.</p

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

Functional Antagonism of WRI1 and TCP20 Modulates \u3ci\u3eGH3.3\u3c/i\u3e Expression to Maintain Auxin Homeostasis in Roots

Auxin is a well-studied phytohormone, vital for diverse plant developmental processes. The GH3 genes are one of the major auxin responsive genes, whose expression changes lead to modulation of plant development and auxin homeostasis. However, the transcriptional regulation of these GH3 genes remains largely unknown. WRI1 is an essential transcriptional regulator governing plant fatty acid biosynthesis. Recently, we identified that the expression of GH3.3 is increased in the roots of wri1-1 mutant. Nevertheless, in this study we found that AtWRI1 did not activate or repress the promoter of GH3.3 (proGH3.3) despite of its binding to proGH3.3. Cross-family transcription factor interactions play pivotal roles in plant gene regulatory networks. To explore the molecular mechanism by which WRI1 controls GH3.3 expression, we screened an Arabidopsis transcription factor library and identified TCP20 as a novel AtWRI1-interacting regulator. The interaction between AtWRI1 and TCP20 was further verified by several approaches. Importantly, we found that TCP20 directly regulates GH3.3 expression via binding to TCP binding element. Furthermore, AtWRI1 repressed the TCP20-mediated transactivation of proGH3.3. EMSAs demonstrated that AtWRI1 antagonized TCP20 from binding to proGH3.3. Collectively, we provide new insights that WRI1 attenuates GH3.3 expression through interaction with TCP20, highlighting a new mechanism that contributes to fine-tuning auxin homeostasis

Small RNA Diversity in Plants and its Impact in Development

MicroRNAs are a class of non-coding RNAs involved in post-transcriptional control of gene expression, either via degradation or translational inhibition of target mRNAs. Both experimental and computational approaches have been used to identify miRNAs and their target genes. In plants, deep sequencing methods have recently allowed the analysis of small RNA diversity in different species and/or mutants. Most sequencing efforts have been concentrated on the identification of miRNAs and their mRNA targets have been predicted based on complementarity criteria. The recent demonstration that certain plant miRNAs could act partly via inhibition of protein translation certainly opens new fields of analysis for plant miRNA function on a broader group of targets. The roles of conserved miRNAs on target mRNA stability have been analysed in different species and defined common mechanisms in development and stress responses. In contrast, much less is known about expression patterns or functions of non-conserved miRNAs. In this review, we focus on the comparative analyses of plant small RNA diversity and the action of si/miRNAs in post-transcriptional regulation of some key genes involved in root development