WGBS Reveals the Dynamic DNA Methylation Turnover in Plant

Introduction

In some eukaryotes, DNA methylation occurs in the coding regions of genes and is called gene body methylation (GbM). Although the role of DNA methylation in transposon and repetitive DNA silencing has been well characterized, gene body methylation is not associated with transcriptional repression, and its biological importance is unknown.

WGBS Service

Whole genome bisulfite sequencing (WGBS) can accurately detect the methylation levels of all individual cytosine bases (C bases) on a genome-wide scale, and is the gold standard for DNA methylation studies. Our WGBS service can provide important technical support for the study of spatiotemporal and temporal specific modifications of genomic DNA methylation, and can be widely used in the study of the mechanism of life processes, such as individual development, aging and disease. WGBS is also the first choice for methylation mapping in various species.

Technical Advantages:

• Wide range of applications: suitable for methylation studies of all species with known reference genomes.
• Genome-wide coverage: maximize access to complete genome-wide methylation information and accurately draw methylation maps.
• Single-base resolution: the methylation status of each C base can be precisely analyzed.

Dynamic DNA Methylation Turnover in Plant

This study was conducted on the model plant Arabidopsis thaliana and revealed that dynamic changes in DNA methylation in plant genebody were associated with enhanced gene expression plasticity by multiomics analysis including WGBS, EM-seq, and RNA-seq. This study reveals a newly identified type of gene body methylation (GbM) in plants, which is subject to constitutive addition and removal of dynamic methylation modifications in all cells including germlines.

Two distinct types of gene body methylation (GbM) in the Arabidopsis genome. (Williams et al., 2023)

Dynamic GbM gene methylation is removed through the demethylation pathway of a family of plant-specific DNA demethylases (collectively known as DRDDases) and added through an unknown source of de novo methylation (most likely the maintenance methyltransferase MET1).

Dynamic GbM genes exhibit methylation heterogeneity in all cell and tissue types. (Williams et al., 2023)

The analysis reveals that the dynamic GbM state exists in homologous genes from different lineages spanning more than 100 million years, indicating evolutionary conservation.

Evolutionary conservation of the Dynamic GbM state. (Williams et al., 2023)

In contrast to other gene body methylation genes, dynamic GbM is closely associated with the presence of promoters or regulatory chromatin states within genes. Dynamic GbM was associated with increased plasticity of gene expression under developmental and different physiological conditions, whereas stably methylated GbM genes showed reduced plasticity. Dynamic GbM genes exhibit reduced dynamics in drdd mutants, suggesting a causal relationship between DNA demethylation and enhanced gene expression plasticity.

Dynamic GbM is associated with increased gene expression plasticity. (Williams et al., 2023)

Reference:

1. Williams, Clara J., et al. "Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity in plants." Genome Biology 24.1 (2023): 227.