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Eriko Sasaki, Magnus Nordborg, The genetic basis of non-CG transposon methylation variation in Arabidopsis thaliana, The 33th International Conference on Arabidopsis Research, 2023.06, A challenge for understanding environmental adaptation is interpretation of genetic and epigenetic variation in natural populations. While variations of DNA cytosine methylation profiles across individuals have been of long-standing interest as a modifier of the genetic code, reflecting past environments or genetic regulation, the establishment processes remain unclear. To address this issue, we dissected an inherited epigenetic mark, non-CG methylation (where H represents A, T, or C), using GWAS approach in Arabidopsis thaliana. Our study revealed that genome-wide mCHG levels are closely associated with de novo methylation (mCHH) and are controlled by major trans-modifiers, including five key trans-regulators CMT2, CMT3, MIR823A, and a novel regulator JMJ26, which specifically regulates RdDM-targeted TEs. The presence of common allelic variation with a large effect suggests some form of local adaptation. Moreover, we present further evidence that allelic variations regulating DNA methylation are associated with transposon mobilization.. |
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Eriko Sasaki, Magnus Nordborg, The genetic basis of inherited DNA methylation variation in natural populations of Arabidopsis thaliana., Integrative Epigenetics in Plants., 2022.12, The epigenome, in a particular variation of DNA methylation profiles across individuals, has long been of interest as a modifier of the genetic code, with “mutations” reflecting past environments, stochastic events, or genetic regulation. To address this question, we dissected the genetic effects on CG methylation over transposable elements as an inherited epigenetics mark. Through GWAS approaches with natural populations of Arabidopsis thaliana, we discovered that CG methylation variation around pericentromeric regions is significantly affected by a genetic variant of a major trans-modifier conserved from mammals to plants. In this presentation, we will discuss a feature of the genetic basis of CG methylation. . |
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Eriko Sasaki, Joanna Gunis, Ilka Reichardt-Gomez, Viktoria Nizhynska, Magnus Nordborg, The genetic basis of inherited DNA methylation variation in Arabidopsis thaliana, Integrative Epigenetics in Plants., 2021.12, The epigenome, in particular variation of DNA methylation profiles across individuals, has long been of interest as a modifier of the genetic code, with “mutations” reflecting past environments, stochastic events, or genetic regulation. To address this issue, we dissected an inherited epigenetics mark, mCHG methylation, using conditional GWAS approaches in Arabidopsis thaliana. Our study revealed the genome-wide mCHG levels largely share the variation with de novo methylation and are under the control of major trans-modifiers, including the key regulators CMT2, CMT3, MIR823A, and a novel regulator JMJ26 that specifically regulated RdDM-targeted TEs.. |
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Eriko Sasaki, The genetic basis of epigenetics in Arabidopsis thaliana, 第43回 日本分子生物学会年会, 2020.12, Transposable element (TE) is one of the major drivers in genome evolution. The ‘selfish mobile elements’ distributing over the genome are considered to influence genome organization, such as genome size, recombination rate, and chromatin structures. Therefore, many species have evolved genome defense system to control TE activities by epigenetic regulation for genome stabilization. DNA cytosine methylation (DNA methylation), a typical epigenetic mark, plays an important role in TE silencing and heterochromatin formation. In plants, it occurs in three sequence contexts: CG, CHG, and CHH (where H is A, T, or C). The latter does not allow direct inheritance of methylation during DNA replication due to lack of symmetry, and methylation must therefore be re-established every cell generation. Genome-wide association studies (GWAS) have shown that CHROMOMETHYLASE2 and NRPE1 as the largest subunit of RNA polymerase V are major determinants of genome-wide patterns of TE CHH methylation. Methylation at TEs targeted by the RNA-directed DNA methylation (RdDM) pathway is unaffected by CMT2 variation, but is strongly affected by variation at NRPE1, which is largely responsible for the longitudinal cline in this phenotype. In contrast, CMT2-targeted TEs are affected by both loci, which jointly explain 7.3% of the phenotypic variation (13.2% of total genetic effects). There is no longitudinal pattern for this phenotype, however, because the geographic patterns appear to compensate for each other in a pattern suggestive of stabilizing selection.. |
