Seasonal Stability and Dynamics of DNA Methylation in Plants in a Natural Environment.

Ito Ito,Kudoh Kudoh,Nishio Nishio,Honjo Honjo,Fujiyama Fujiyama,Tarutani Tarutani,Toyoda Toyoda,Kakutani Kakutani,Emura Emura

doi:10.3390/genes10070544

Abstract

DNA methylation has been considered a stable epigenetic mark but may respond to fluctuating environments. However, it is unclear how they behave in natural environments. Here, we analyzed seasonal patterns of genome-wide DNA methylation in a single clone from a natural population of the perennial Arabidopsis halleri. The genome-wide pattern of DNA methylation was primarily stable, and most of the repetitive regions were methylated across the year. Although the proportion was small, we detected seasonally methylated cytosines (SeMCs) in the genome. SeMCs in the CHH context were detected predominantly at repetitive sequences in intergenic regions. In contrast, gene-body CG methylation (gbM) itself was generally stable across seasons, but the levels of gbM were positively associated with seasonal stability of RNA expression of the genes. These results suggest the existence of two distinct aspects of DNA methylation in natural environments: sources of epigenetic variation and epigenetic marks for stable gene expression.

Highlights

DNA methylation at cytosine residues is an epigenetic mark that can be maintained through cell divisions in a wide range of eukaryotic genomes [1]
We examined the seasonal patterns of DNA methylation at CG, CHG, and CHH
The advantage of our study is that we captured dynamics DNA methylation at all seasonal phases that plants experience under natural conditions

Summary

Introduction

DNA methylation at cytosine residues is an epigenetic mark that can be maintained through cell divisions in a wide range of eukaryotic genomes [1]. DNA-methylation varies both between and within species [8], and sometimes is associated with phenotypic variation [9,10,11]. The level and patterns of DNA methylation are heritable to a certain extent, the mechanisms that produce and maintain epigenetic variation across generations are largely unknown. DNA methylation can vary between individuals by non-genetic causes. Because of its semi-stable and semi-labile nature, non-genetic changes in DNA methylation are not explained by simple environmental effects. Even in a genetically homogeneous background under stable laboratory conditions, epigenetic variation in DNA methylation can occur during repeated self-pollination in

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Conclusion