Laanen Pol, Saenen Eline, Mysara Mohamed, Van de Walle Jorden, Van Hees May, Nauts Robin, Van Nieuwerburgh Filip, Voorspoels Stefan, Jacobs Griet, Cuypers Ann, Horemans Nele
Biosphere Impact Studies, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium.
Centre for Environmental Research, Hasselt University, Diepenbeek, Belgium.
Front Plant Sci. 2021 Mar 31;12:611783. doi: 10.3389/fpls.2021.611783. eCollection 2021.
Previous studies have found indications that exposure to ionising radiation (IR) results in DNA methylation changes in plants. However, this phenomenon is yet to be studied across multiple generations. Furthermore, the exact role of these changes in the IR-induced plant response is still far from understood. Here, we study the effect of gamma radiation on DNA methylation and its effect across generations in young plants. A multigenerational set-up was used in which three generations (Parent, generation 1, and generation 2) of 7-day old plants were exposed to either of the different radiation treatments (30, 60, 110, or 430 mGy/h) or to natural background radiation (control condition) for 14 days. The parental generation consisted of previously non-exposed plants, whereas generation 1 and generation 2 plants had already received a similar irradiation in the previous one or two generations, respectively. Directly after exposure the entire methylomes were analysed with UPLC-MS/MS to measure whole genome methylation levels. Whole genome bisulfite sequencing was used to identify differentially methylated regions (DMRs), including their methylation context in the three generations and this for three different radiation conditions (control, 30 mGy/h, and 110 mGy/h). Both intra- and intergenerational comparisons of the genes and transposable elements associated with the DMRs were made. Taking the methylation context into account, the highest number of changes were found for cytosines followed directly by guanine (CG methylation), whereas only limited changes in CHG methylation occurred and no changes in CHH methylation were observed. A clear increase in IR-induced DMRs was seen over the three generations that were exposed to the lowest dose rate, where generation 2 had a markedly higher number of DMRs than the previous two generations (Parent and generation 1). Counterintuitively, we did not see significant differences in the plants exposed to the highest dose rate. A large number of DMRs associated with transposable elements were found, the majority of them being hypermethylated, likely leading to more genetic stability. Next to that, a significant number of DMRs were associated with genes (either in their promoter-associated region or gene body). A functional analysis of these genes showed an enrichment for genes related to development as well as various stress responses, including DNA repair, RNA splicing, and (a)biotic stress responses. These observations indicate a role of DNA methylation in the regulation of these genes in response to IR exposure and shows a possible role for epigenetics in plant adaptation to IR over multiple generations.
先前的研究已发现一些迹象，表明植物暴露于电离辐射（IR）会导致DNA甲基化发生变化。然而，这一现象尚未在多代植物中进行研究。此外，这些变化在IR诱导的植物反应中的确切作用仍远未明确。在此，我们研究了γ辐射对DNA甲基化的影响及其在幼龄植物中的跨代效应。我们采用了多代设置，将7日龄植物的三代（亲代、第1代和第2代）暴露于不同的辐射处理（30、60、110或430 mGy/h）或自然背景辐射（对照条件）下14天。亲代由先前未暴露的植物组成，而第1代和第2代植物分别在前一代或两代中已接受过类似的辐照。暴露后立即用超高效液相色谱-串联质谱（UPLC-MS/MS）分析整个甲基化组，以测量全基因组甲基化水平。全基因组亚硫酸氢盐测序用于鉴定差异甲基化区域（DMR），包括三代植物中它们的甲基化背景，以及三种不同辐射条件（对照、30 mGy/h和110 mGy/h）下的情况。对与DMR相关的基因和转座元件进行了代内和代际比较。考虑到甲基化背景，发现胞嘧啶的变化数量最多，其次是鸟嘌呤（CG甲基化），而CHG甲基化仅发生有限变化，未观察到CHH甲基化的变化。在暴露于最低剂量率的三代植物中，IR诱导的DMR明显增加，其中第2代的DMR数量明显高于前两代（亲代和第1代）。与直觉相反，在暴露于最高剂量率的植物中我们未观察到显著差异。发现大量与转座元件相关的DMR，其中大多数发生了高甲基化，这可能导致更高的遗传稳定性。除此之外，大量DMR与基因相关（要么在其启动子相关区域，要么在基因体中）。对这些基因的功能分析表明，与发育以及各种应激反应相关的基因富集，包括DNA修复、RNA剪接和（生物或非生物）应激反应。这些观察结果表明DNA甲基化在响应IR暴露时对这些基因的调控中发挥作用，并显示了表观遗传学在植物多代适应IR过程中的可能作用。
