TEA: the epigenome platform for Arabidopsis methylome study

Area of Science:

• Plant Genomics
• Epigenetics
• Bioinformatics

Background:

• Bisulfite sequencing (BS-seq) enables genome-wide DNA methylation profiling at single-base resolution.
• BS-seq data analysis and visualization are complex due to numerous features and sequence contexts.
• Applications include genomic imprinting, transcriptional regulation, and cellular development studies.

Purpose of the Study:

• To develop a streamlined platform, TEA, for analyzing and visualizing whole-genome BS-Seq (WGBS) data from Arabidopsis thaliana.
• To introduce an efficient method for measuring genome methylation in each sequence context by gene.
• To provide an intuitive and efficient online platform for exploring Arabidopsis DNA methylation.

Main Methods:

• Developed a Java-scripted platform (TEA) to process BS-Seq mapping results.
• Implemented a straightforward method for measuring genome methylation by gene and sequence context.
• Created a web-based platform with data uploading capabilities, linked to an Arabidopsis annotation database and toolkits.

Main Results:

• TEA processes BS-Seq mapping results efficiently.
• The platform measures genome methylation levels in each sequence context by gene.
• TEA provides a web-based interface for deep analysis of WGBS data.

Conclusions:

• TEA is an intuitive and efficient online platform for analyzing the Arabidopsis genomic DNA methylation landscape.
• The platform offers multiple functionalities for users to exploit WGBS data.
• TEA is freely accessible to academic users at http://tea.iis.sinica.edu.tw.