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ppdb: a plant promoter database

ppdb: a plant promoter database,10.1093/nar/gkm785,Nucleic Acids Research,Yoshiharu Y. Yamamoto,Junichi Obokata

ppdb: a plant promoter database   (Citations: 17)
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ppdb (http://www.ppdb.gene.nagoya-u.ac.jp) is a plant promoter database that provides promoter annotation of Arabidopsis and rice. The database contains information on promoter structures, transcription start sites (TSSs) that have been identified from full-length cDNA clones and also a vast amount of TSS tag data. In ppdb, the promoter structures are determined by sets of promoter elements identified by a position-sensitive extrac- tion method called local distribution of short sequences (LDSS). By using this database, the core promoter structure, the presence of regulatory elements and the distribution of TSS clusters can be identified. Although no differentiation of promoter architecture among plant species has been reported, there is some divergence of utilized sequences for promoter elements. Therefore, ppdb is based on species-specific sets of promoter elements, rather than on general motifs for multiple species. Each regulatory sequence is hyperlinked to literary information, a PLACE entry served by a plant cis-element database, and a list of promoters containing the regulatory sequence. BACKGROUND A promoter database can be generated from a combina- tion of genome sequence, information of promoter positions and a list of cis-regulatory elements. Currently a major restriction on the quality of a promoter database is our limited knowledge of cis-elements. There are several established genome-wide plant promoter databases avail- able today (RARGE: (1), http://www.rarge.gsc.riken.jp/; AGRIS: (2), http://www.arabidopsis.med.ohio-state.edu/; AthaMap: (3), http://www.athamap.de/), and which are based on cis-regulatory sequences from PlantCARE ((4), http://www.bioinformatics.psb.ugent.be/webtools/ plantcare/html/), PLACE ((5), http://www.dna.affrc. go.jp/PLACE/) or TRANSFAC ((6), http://www.gene- regulation.com/pub/databases.html). These three promo- ter databases focus on cis-regulatory elements rather than core promoter structure, aiming to reveal the regulatory machinery that give the expression profiles. Unfortunately, these databases provide information only for Arabidopsis, and there are no genome-wide plant promoter databases available for other plant species. Local distribution of short sequences (LDSS) analysis is a method to extract promoter constituents by genome- wide statistical analysis (7,8). We have applied this method to the Arabidopsis and rice genomes, and identified 1000 octamer sequences per genome as LDSS-positive promoter elements (8). According to their distribution profiles, the identified octamers have been classified into regulatory element group (REG), TATA box and Y Patch as three major promoter element groups. REG is a direction-insensitive element that is preferentially found around 100 bp relative to the major transcription start site (TSS), and contains many established cis-regulatory sequences. Y Patch is a direction-sensitive plant core promoter element that appears around TSS. We found that utilized sequences of all three groups, including TATA element, are moderately differentiated between Arabidopsis and rice, demonstrating the importance of individual preparation of promoter elements for each genome. The large collection of extracted promoter elements can be utilized as a tool to reveal precise promoter architec- ture. Therefore, here we present a novel searchable ppdb database, based on the LDSS-positive elements. Utilization of a genome-specific set of promoter elements and the detection of the core promoter structure are the two unique features of this database. Currently, ppdb is the only one plant promoter database with information about core promoter types on a genomic scale, and the first genome-wide database for rice promoters.
Journal: Nucleic Acids Research - NAR , vol. 36, no. Database-I, pp. 977-981, 2008
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    • ...The second blue line shows information form the ppdb [19], and the database identify positions of REGs and a TATA box in the promoter...
    • ...All the REGs identified in these analyses are shown in Table 4. These data will be incorporated to our promoter database, the ppdb [19] in the near future...
    • ...The major TSS was determined by large scale TSS tag sequencing [8] or 5’ end information of RAFL cDNA clones [19,31]...
    • ...The promoters containing the REGs shown in Table 4 can be viewed at the ppdb (Plant Promoter Database, [19,36])...

    Yoshiharu Y Yamamotoet al. Prediction of transcriptional regulatory elements for plant hormone re...

    • ...In search of cis-elements in the promoter of puf and 2cpb In silico analysis of the divergent promoter was performed looking for cis-elements using the Plant Promoter Database (ppdb) [25], PlantCARE [26], PLACE [27], and Athamap [28] web tools...
    • ...They are: one heat shock element (CCAAT box), a Y Patch found in the majority of Arabidopsis promoters but with unknown function [25], and three binding sites of homeodomainsleucine zipper transcription factors, some of them being able to bind in both directions [27,28]...

    Hernán G Bondinoet al. A small intergenic region drives exclusive tissue-specific expression ...

    • ...Data for this analysis was obtained from ppdb (plant promoter database; Yamamoto, Obokata 2008) a Promoter sequences encompassed bases from 1000 residues upstream of the ATG codon to 200 residues downstream of the ATG codon...

    Jennifer D. Hallet al. UVH6, a Plant Homolog of the Human/Yeast TFIIH Transcription Factor Su...

    • ...The core promoter structure, presence of cis-acting regulatory elements, and distribution of transcription start site clusters can also be viewed (Yamamoto and Obokata 2008)...

    Olga G. Smirnovaet al. Simple database to select promoters for plant transgenesis

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