DNA methylome analysis provides evidence that the expansion of the tea genome is linked to TE bursts.

Lei Wang,Shengli Jing,Xiaojun Chang,Qunjie Zhang,Chenjiang You,Haifeng Wang,Yan Shi,Hongyu Yuan

doi:10.1111/pbi.13018

Abstract

Summary DNA methylation is essential for gene regulation, imprinting and silencing of transposable elements (TEs). Although bursts of transposable elements are common in many plant lineages, how plant DNA methylation is related to transposon bursts remains unclear. Here we explore the landscape of DNA methylation of tea, a species thought to have experienced a recent transposon burst event. This species possesses more transposable elements than any other sequenced asterids (potato, tomato, coffee, pepper and tobacco). The overall average DNA methylation levels were found to differ among the tea, potato and tomato genomes, and methylation at CHG sequence sites was found to be significantly higher in tea than that in potato or tomato. Moreover, the abundant TEs resulting from burst events not only resulted in tea developing a very large genome size, but also affected many genes involved in importantly biological processes, including caffeine, theanine and flavonoid metabolic pathway genes. In addition, recently transposed TEs were more heavily methylated than ancient ones, implying that DNA methylation is proportionate to the degree of TE silencing, especially on recent active ones. Taken together, our results show that DNA methylation regulates transposon silencing and may play a role in genome size expansion.

Highlights

DNA methylation is a stable epigenetic mark that is widespread among eukaryotic species
De novo establishment of DNA methylation in all three contexts is mediated by the RNA-directed DNA methylation (RdDM) pathway guided by small RNAs and domains rearranged methyltransferase 2 (DRM2) (Cao and Jacobsen, 2002)
Genetic studies of the model plant Arabidopsis thaliana have defined many of the key components involved in the DNA methylation pathways, including methyltransferase 1 (MET1), DRM2, CMT2, and chromomethylase 3 (CMT3) (Law and Jacobsen, 2010; Matzke et al, 2015)

Summary

Introduction

DNA methylation is a stable epigenetic mark that is widespread among eukaryotic species. Extensive studies have shown that DNA methylation plays an important role in regulation gene expression and transposon silencing (Finnegan et al, 2000; Gehring and Henikoff, 2007). CHH methylation is established and maintained by CMT2, and like CHG methylation, it is associated with methylation in H3K9me regions (Gouil and Baulcombe, 2016). De novo establishment of DNA methylation in all three contexts is mediated by the RNA-directed DNA methylation (RdDM) pathway guided by small RNAs and domains rearranged methyltransferase 2 (DRM2) (Cao and Jacobsen, 2002). CMT2 plays a role in CHG methylation (Law and Jacobsen, 2010; Stroud et al, 2013)

Results

Discussion

Conclusion