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

1
Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
2
Department of Chromosome Science, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
3
Department of Environmental Sciences and Technology, Faculty of Agriculture, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-0065, Japan
4
Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
5
Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
6
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
*
Author to whom correspondence should be addressed.
Genes 2019, 10(7), 544; https://doi.org/10.3390/genes10070544
Received: 19 June 2019 / Revised: 14 July 2019 / Accepted: 15 July 2019 / Published: 17 July 2019
(This article belongs to the Section Plant Genetics and Genomics)
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. View Full-Text
Keywords: Arabidopsis halleri; DNA methylation; natural environment; seasonal changes; seasonally methylated cytosines Arabidopsis halleri; DNA methylation; natural environment; seasonal changes; seasonally methylated cytosines
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Ito, T.; Nishio, H.; Tarutani, Y.; Emura, N.; Honjo, M.N.; Toyoda, A.; Fujiyama, A.; Kakutani, T.; Kudoh, H. Seasonal Stability and Dynamics of DNA Methylation in Plants in a Natural Environment. Genes 2019, 10, 544.

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