Contribution of RdDM to the ecotype-specific differential methylation on conserved as well as highly variable regions between Arabidopsis ecotypes

BMC Genomics

Research

Kyunghyuk Park¹  Choongwon Jeong¹  Haechan Gill¹  Youbong Hyun²  Yeonhee Choi²  Jaehoon Lee²  Jong-Seong Jeon³  Sang-Kyu Lee⁴  Sang-Yoon Shin⁵  Chanseok Shin⁶ 

[1]Department of Biological Sciences, Seoul National University, 08826, Seoul, South Korea

[2]Department of Biological Sciences, Seoul National University, 08826, Seoul, South Korea

[3]Research Center for Plant Plasticity, Seoul National University, 08826, Seoul, Republic of Korea

[4]Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, 17104, Yongin, South Korea

[5]Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, 17104, Yongin, South Korea

[6]Current address: Division of Life Science, Gyeongsang National University, 52828, Jinju, South Korea

[7]Research Center for Plant Plasticity, Seoul National University, 08826, Seoul, Republic of Korea

[8]Interdisciplinary Program in Agricultural Genomics, Seoul National University, 08826, Seoul, Republic of Korea

[9]Research Center for Plant Plasticity, Seoul National University, 08826, Seoul, Republic of Korea

[10]Interdisciplinary Program in Agricultural Genomics, Seoul National University, 08826, Seoul, Republic of Korea

[11]Department of Agricultural Biotechnology, Seoul National University, 08826, Seoul, Republic of Korea

[12]Research Institute of Agriculture and Life Sciences, Seoul National University, 08826, Seoul, Republic of Korea

[13]Plant Genomics and Breeding Institute, Seoul National University, 08826, Seoul, South Korea

关键词: Arabidopsis;    Methylome;    Transposable elements (TEs);    Structural variation;    RNA-directed DNA methylation (RdDM);   

DOI  :  10.1186/s12864-023-09128-4

 received in 2022-11-10, accepted in 2023-01-11,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundSeveral studies showed genome-wide DNA methylation during Arabidopsis embryogenesis and germination. Although it has been known that the change of DNA methylation mainly occurs at CHH context mediated by small RNA-directed DNA methylation pathway during seed ripening and germination, the causality of the methylation difference exhibited in natural Arabidopsis ecotypes has not been thoroughly studied.ResultsIn this study we compared DNA methylation difference using comparative pairwise multi-omics dynamics in Columbia-0 (Col) and Cape Verde Island (Cvi) ecotypes. Arabidopsis genome was divided into two regions, common regions in both ecotypes and Col-specific regions, depending on the reads mapping of whole genome bisulfite sequencing libraries from both ecotypes. Ecotype comparison was conducted within common regions and the levels of DNA methylation on common regions and Col-specific regions were also compared. we confirmed transcriptome were relatively dynamic in stage-wise whereas the DNA methylome and small RNAome were more ecotype-dependent. While the global CG methylation remains steady during maturation and germination, we found genic CG methylation differs the most between the two accessions. We also found that ecotype-specific differentially methylated regions (eDMR) are positively correlated with ecotype-specifically expressed 24-nt small RNA clusters. In addition, we discovered that Col-specific regions enriched with transposable elements (TEs) and structural variants that tend to become hypermethylated, and TEs in Col-specific regions were longer in size, more pericentromeric, and more hypermethylated than those in the common regions. Through the analysis of RdDM machinery mutants, we confirmed methylation on Col-specific region as well as on eDMRs in common region are contributed by RdDM pathway. Lastly, we demonstrated that highly variable sequences between ecotypes (HOT regions) were also affected by RdDM-mediated regulation.ConclusionsThrough ecotype comparison, we revealed differences and similarities of their transcriptome, methylome and small RNAome both in global and local regions. We validated the contribution of RdDM causing differential methylation of common regions. Hypermethylated ecotype-specific regions contributed by RNA-directed DNA methylation pathway largely depend on the presence of TEs and copy-gain structural variations. These ecotype-specific regions are frequently associated with HOT regions, providing evolutionary insights into the epigenome dynamics within a species.

【 授权许可】

CC BY   
© The Author(s) 2023

【 图 表 】

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