Epigenetic regulation of ecotype-specific expression of the heat-activated transposon ONSEN

Abstract

Transposable elements are present in a wide variety of organisms; however, our understanding of the diversity of mechanisms involved in their activation is incomplete. In this study, we analyzed the transcriptional activation of the ONSEN retrotransposon, which is activated by high-temperature stress in Arabidopsis thaliana. We found that its transcription is significantly higher in the Japanese ecotype Kyoto. Considering that transposons are epigenetically regulated, DNA methylation levels were analyzed, revealing that CHH methylation was reduced in Kyoto compared to the standard ecotype, Col-0. A mutation was also detected in the Kyoto CMT2 gene, encoding a CHH methyltransferase, suggesting that it may be responsible for increased expression of ONSEN. CHH methylation is controlled by histone modifications through a self-reinforcing loop between DNA methyltransferase and histone methyltransferase. Analysis of these modifications revealed that the level of H3K9me2, a repressive histone marker for gene expression, was lower in Kyoto than in Col-0. The level of another repressive histone marker, H3K27me1, was decreased in Kyoto; however, it was not impacted in a Col-0 cmt2 mutant. Therefore, in addition to the CMT2 mutation, other factors may reduce repressive histone modifications in Kyoto.

Natural diversity of heat-induced transcription of retrotransposons inArabidopsis thaliana

“…The strong variation in the activity of Copia-35, which is equally abundant in all three accessions but differentially expressed, is in line with previous work (Marí-Ordóñez et al 2013; Thieme et al 2017; Nozawa et al 2022), and suggests that factors other than copy number determine the overall activity of a TE-family. For instance, Copia-35 expression increases in mutants deficient in epigenetic silencing (Yokthongwattana et al 2010) while the loss of RdDM alone (i.e without abiotic stress), does not activate ONSEN (Ito et al 2011), highlighting differences in the factors governing the activities of both families.…”

“…For instance, Copia-35 expression increases in mutants deficient in epigenetic silencing (Yokthongwattana et al 2010) while the loss of RdDM alone (i.e without abiotic stress), does not activate ONSEN (Ito et al 2011), highlighting differences in the factors governing the activities of both families. Notably, recent work showed that natural variations in the strength of epigenetic silencing under heat stress leads to increased activation of ONSEN in the Kyoto accession that displays reduced methylation in the CHH context (Nozawa et al 2022). In this regard, it is noteworthy that the relic accession Cvi-0 that displayed a high activity of both TEs in our study is globally hypomethylated compared to Col-0 (Kawakatsu et al 2016).…”

Barley AGO4 proteins show overlapping functionality with distinct small RNA-binding properties in heterologous complementation

“…The relative quantification of Ty1 / copia -like retrotransposon ATCOPIA78 ( ONSEN ) copies was performed using non-treated Arabidopsis wild-type DNA as a control, and in relation to its quantification consisting of eight ONSEN copies in the Col-0 ecotype genome (Ito et al 2011 , 2013 ; Hayashi et al 2020 ; Nozawa et al 2022 ), all relative amounts of the other non-treated and heat-stressed samples were measured using qPCR. Analysis by qPCR was performed using the Luminaris Color HiGreen qPCR Master Mix (Thermo Fisher Scientific) with 20 ng of genomic DNA per reaction and the LightCycler 96 Instrument real-time PCR machine (Roche).…”

Single molecule long-read eccDNA sequencing reveals unambiguous and selective transposon activation in Arabidopsis in response to stress, cellular state, and epigenetic processes

“…ONSEN primarily targets euchromatin regions for insertion and can impact gene expression (Ito et al, 2016). Recent studies have shown that DNA methylation, specifically CHH methylation, and repressive histone modifications, H3K9me2 and H3K27me1, are linked to ONSEN expression and transposition (Nozawa et al, 2021(Nozawa et al, , 2022. Because of these properties, protocols have been developed to induce the activation of ONSEN, for example by inhibiting RNA polymerase II (Thieme et al, 2017), and utilized to demonstrate that the mobilization of a single TE family can increase the size of the host genome and contribute to a wide range of transcriptomic novelty (Roquis et al, 2021).…”