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Plant Promoter Analysis: Identification and Characterization of Root Nodule Specific Promoter in the Common Bean
Published on: December 23, 2017
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Plant Promoter Database (PPDB).
Kazutaka Kusunoki1, Yoshiharu Y Yamamoto2,3,4,5
1United Graduate School of Agricultural Science, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan.
Methods in Molecular Biology (Clifton, N.J.)
|December 18, 2016
Summary
The Plant Promoter Database (PPDB) offers comprehensive promoter information for key plant species. It integrates bioinformatically identified core promoter elements and regulatory elements with experimental transcription start site data.
Area of Science:
- Plant genomics
- Bioinformatics
- Molecular biology
Background:
- Understanding gene regulation is crucial for plant science.
- Plant promoter regions contain essential regulatory elements.
- Existing databases may lack comprehensive, integrated promoter data.
Purpose of the Study:
- To develop and present the Plant Promoter Database (PPDB).
- To provide a centralized resource for plant gene promoter information.
- To integrate bioinformatic and experimental data for promoter analysis.
Main Methods:
- Genome sequence annotation using identified octamer motifs.
- Identification of core promoter elements (TATA boxes, Initiators, etc.) and regulatory element groups (REGs).
- Utilizing Local Distribution of Short Sequence (LDSS) analysis for element identification.
- Integration with the PLACE database and gene expression data for functional insights.
Main Results:
- PPDB provides promoter information for Arabidopsis, rice, poplar, and Physcomitrella patens.
- The database annotates genome sequences with core promoter structures and regulatory elements.
- Promoter elements are identified based on biased localization profiles.
- Regulatory elements are linked to physiological roles predicted from gene expression data.
Conclusions:
- PPDB serves as a valuable resource for plant promoter research.
- The integration of diverse data types enhances promoter analysis.
- The database facilitates a deeper understanding of gene regulation in plants.
