ppdb: plant promoter database version 3.0

Abstract

ppdb (http://ppdb.agr.gifu-u.ac.jp) is a plant promoter database that provides information on transcription start sites (TSSs), core promoter structure (TATA boxes, Initiators, Y Patches, GA and CA elements) and regulatory element groups (REGs) as putative and comprehensive transcriptional regulatory elements. Since the last report in this journal, the database has been updated in three areas to version 3.0. First, new genomes have been included in the database, and now ppdb provides information on Arabidopsis thaliana, rice, Physcomitrella patens and poplar. Second, new TSS tag data (34 million) from A. thaliana, determined by a high throughput sequencer, has been added to give a ∼200-fold increase in TSS data compared with version 1.0. This results in a much higher coverage of ∼27 000 A. thaliana genes and finer positioning of promoters even for genes with low expression levels. Third, microarray data-based predictions have been appended as REG annotations which inform their putative physiological roles.

Stomatal Guard Cells Co-opted an Ancient ABA-Dependent Desiccation Survival System to Regulate Stomatal Closure

“…Both the cis-regulatory ABA-responsive promoter elements (ABREs) and homologs of transacting factors from the ABF/ABI5 subfamily of bZIP transcription factors binding to ABREs in promoters of ABA-responsive genes have been found in the moss Physcomitrella [19,[24][25][26]. To gain deeper insights into the evolution of fast ABA signaling leading to stomatal closure, we asked the following question: when did early land plants start to use the ancient ABA-dependent drought stress-signaling pathway to control stomatal transpiration ( Figure 1B)?…”

SENSITIVE TO PROTON RHIZOTOXICITY1, CALMODULIN BINDING TRANSCRIPTION ACTIVATOR2, and Other Transcription Factors Are Involved inALUMINUM-ACTIVATED MALATE TRANSPORTER1Expression

“…The RAR was calculated as the ratio of the frequency of each octamer unit in the promoter of the grouped genes to that in the promoters of genome-wide genes. The promoter was defined as -1,000 bp from the TSS reported in the Plant Promoter Database (ppdb; http://ppdb.agr.gifu-u.ac.jp; Hieno et al, 2014). The RAR value of each octamer unit was plotted on the 0-to -540-bp region of the AtALMT1 promoter and statistical significance (P , 0.05) was assessed with Fisher's exact test.…”

The Responses of Arabidopsis Early Light-Induced Protein2 to Ultraviolet B, High Light, and Cold Stress Are Regulated by a Transcriptional Regulatory Unit Composed of Two Elements

“…As a first step, we searched the database composed of 24,956 promoters (Hieno et al, 2014) for genes containing Elements A and B in the promoter region. A total of 236 genes containing Element A and 71 genes containing Element B in the promoter region was identified (Supplemental Table S1).…”

“…The promoter sequences used for prediction in this study included a set of 14,959 promoters whose positions have been experimentally identified (Yamamoto et al, , 2011 or a new set composed of 24,956 promoters redetermined by sequencing of 34 million transcription start site tags (Hieno et al, 2014). This analysis evaluates the degree of overrepresentation of each octamer in some stressresponsive promoters identified by microarray analysis over total promoters in an analyzed genome.…”