MethGET: web-based bioinformatics software for correlating genome-wide DNA methylation and gene expression

Area of Science:

• Epigenetics
• Bioinformatics
• Genomics

Background:

• DNA methylation is a key epigenetic regulator of gene expression, with its effects varying by genomic location and species.
• Existing bioinformatics tools primarily focus on CG methylation and human genomes, limiting the analysis of non-CG methylation and diverse species.
• Understanding the correlation between DNA methylation and gene expression is vital for deciphering regulatory roles.

Purpose of the Study:

• To develop a versatile bioinformatics web tool for analyzing genome-wide DNA methylation and gene expression correlations.
• To enable analysis of CG, CHG, and CHH methylation across any genome using user-provided data.
• To facilitate both single-sample and comparative analyses of methylation-expression relationships.

Main Methods:

• Development of MethGET, a web-based bioinformatics tool utilizing whole-genome bisulfite sequencing data.
• Implementation of single-methylome analyses (Pearson correlations, ordinal associations) and multiple-methylome analyses (comparative analyses, heatmaps).
• Application of MethGET to rice regeneration data to investigate epigenetic regulation in tissue culture.

Main Results:

• MethGET is the first web tool allowing users to analyze DNA methylation and gene expression correlations for any genome, including non-CG sites (CHG, CHH).
• The tool supports single-methylome analysis, revealing correlations within samples, and multiple-methylome analysis for group comparisons.
• Analysis of rice data revealed potential roles for CHH methylation in gene bodies during tissue culture, showcasing MethGET's utility in epigenomic research.

Conclusions:

• MethGET is a user-friendly Python software with a web interface and a stand-alone version for correlating DNA methylation and gene expression.
• The tool supports comprehensive analysis of various methylation contexts (CG, CHG, CHH) across diverse genomes.
• MethGET provides valuable insights into epigenomic regulation and is publicly available for research use.