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Machine learning analyses of methylation profiles uncovers tissue-specific gene expression patterns in wheat
Amidou N'Diaye1, Brook Byrns1, Aron T Cory1
1Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8.
The Plant Genome
|October 5, 2020
Summary
DNA methylation impacts gene expression in wheat. Promoter, CDS, and exon methylation in the CG context significantly influence tissue-specific gene regulation, aiding in identifying differentially expressed genes.
Area of Science:
- Plant molecular biology
- Epigenetics
- Genomics
Background:
- DNA methylation is a key epigenetic regulator of gene expression in eukaryotes.
- Gene promoter methylation typically represses transcription, while gene body methylation is linked to active transcription.
- The interplay between methylation across different genic regions and its impact on gene regulation remains incompletely understood.
Purpose of the Study:
- To investigate the interaction between DNA methylation levels across genic regions in bread wheat (Triticum aestivum).
- To identify differentially expressed genes (DEGs) between roots and leaves and determine the impact of methylation on their regulation.
- To uncover which methylation sites have the most significant effect on gene expression.
Main Methods:
- Analysis of DNA methylation patterns in the bread wheat cultivar Chinese Spring.
- Application of six machine learning algorithms and a deep neural network to predict DEGs.
- Correlation analysis of methylation levels across genic regions (promoter, CDS, exon, etc.) and gene expression.
Main Results:
- Genes with higher leaf expression were associated with photosynthesis and pigment biosynthesis.
- Methylation predominantly occurred in the CG context (60%), followed by CHG (35%) and CHH (5%).
- Methylation levels were highly correlated across genic regions, except for the promoter.
- Machine learning models achieved high prediction accuracy (0.81) for DEGs.
- Methylation in the promoter, CDS, and exon in the CG context showed the most significant impact on gene regulation.
Conclusions:
- DNA methylation across all genic regions contributes to gene regulation in wheat.
- Promoter, CDS, and exon methylation in the CG context are critical determinants of tissue-specific gene expression.
- Methylation profiles can be utilized to identify tissue-specific genes, offering insights into gene regulation mechanisms.
