PlantDHS: a database for DNase I hypersensitive sites in plants

Area of Science:

• Genomics
• Plant Biology
• Bioinformatics

Background:

• Gene expression relies on regulatory proteins binding to cis-regulatory elements (CREs).
• Existing plant databases primarily focus on promoters, neglecting other crucial CREs.
• A comprehensive resource for investigating all plant CREs is needed.

Purpose of the Study:

• To introduce PlantDHS, a novel database for exploring all plant cis-regulatory elements (CREs).
• To integrate diverse genomic data, including histone modifications and transcription factor binding sites, for CRE analysis.
• To provide a user-friendly platform for predicting CREs in model plant species.

Main Methods:

• Developed PlantDHS, a web-accessible database (http://plantdhs.org).
• Integrated DNase I hypersensitive site (DHS) data with histone modification, RNA sequencing, nucleosome positioning, and transcription factor binding site information.
• Focused on three model plant species: Arabidopsis thaliana, Brachypodium distachyon, and rice (Oryza sativa).

Main Results:

• PlantDHS identifies DNase I hypersensitive sites (DHSs) as indicators of all CREs (promoters, enhancers, silencers, insulators, TF binding sites).
• The database facilitates the prediction of CREs associated with individual genes.
• PlantDHS is particularly effective in detecting distal CREs located far from gene promoters.

Conclusions:

• PlantDHS offers a valuable resource for studying global gene expression regulation in plants.
• The database enhances the ability to discover and analyze both proximal and distal CREs.
• PlantDHS supports comprehensive investigations into plant cis-regulatory element function and organization.