Epigenetic regulation of ecotype-specific expression of a heat-activated transposon

Transposable elements (TEs) are mobile genes that are conserved in a wide variety of organisms, but the diversity of their activation has not been well studied. In this study, we analyzed the diversity in the transcriptional level of a retrotransposon called ONSEN, which is activated by high temperature stress in Arabidopsis thaliana. We found that the transcript level of ONSEN is significantly higher in the Japanese ecotype, Kyoto. Since transposons are epigenetically regulated, DNA methylation levels were analyzed, and revealed that CHH methylation was reduced in Kyoto compared to the standard ecotype, Col-0. A mutation was found in the sequence of CMT2, a CHH methyltransferase in Kyoto. This suggests that the mutation of CMT2 is the responsible for the high expression of ONSEN in Kyoto. CHH methylation forms a feedback loop with histone modifications to complement each other's modifications. Analysis of the histone modifications revealed that H3K9me2, a repressive histone mark for gene expression, was decreased in Kyoto compared to Col-0. Furthermore, another repressive histone mark, H3K27me1, was also decreased, but not in the cmt2 mutant of Col-0. Therefore, in addition to the CMT2 mutation, there may be other factors that reduce repressive histone modifications in Kyoto.