Multi-omics profiling reveals ethylene signalling as a key pathway underlying both genetic and epigenetic responses to low-dose ionizing radiation in Arabidopsis

There is increasing interest in the effects of low-dose ionizing radiation (IR) on plants as might occur during spaceflight, or as a consequence of human activities, such as nuclear power generation, that may result in the release of radioactive materials into the environment. High doses of IR have long been used for the induction of mutations in plants with the goal of generating desirable traits for agribusiness. However, less is known about the responses of plants to acute low doses of IR exposure. Here, we take a multi-omics approach to characterize the response to low dose IR in A. thaliana. We adapt the Methyltransferase Accessibility Protocol for individual templates (MAPit) technique for use in plants allowing us to assay the epigenetic response to acute low-dose IR (10 cGy and 100 cGy) 72 hr after exposure, and, in parallel, use RNA sequencing to profile the transcription response at 1, 3, 24 and 72 hr after exposure. We observe that IR exposures as low as 10 cGy elicit robust genetic responses in Arabidopsis thaliana detectable as early as 1 hr after exposure. Examination of these responses revealed dose-dependent changes in gene expression, chromatin accessibility and DNA methylation that implicate the ethylene signalling pathway and response to abiotic stress as underlying the transcriptional and epigenetic changes associated with IR. These changes are observable up to 72 hr after exposure suggesting that they are maintained well after the initial acute exposure. Our findings indicate that A. thaliana executes a coordinated, multi-modal response to low-dose IR through induction and regulation of the ethylene response pathway. Overall design: To investigate the effect of low-dose ionizing radiation on gene expression in Arabidopsis thaliana (Col-0 ecotype), A. thaliana seeds were sown in autoclaved soil and cold-treated at 4°C for 3 days to promote uniform germination (Zhou et al., 2017). Plants were grown under a short-day condition (8 hr light, 16 hr dark) at 22°C for 1 week, followed by transplantation of each seedling to individual cells in 36-cell trays At 4 weeks of growth, plants were placed in a 137Cs irradiator and exposed to gamma IR at 1.4 cGy per second. Plants were irradiated for 7 sec (10 cGy equivalent), 71 sec (100 cGy equivalent) or not exposed (0 cGy or “Mock”). Gene expression profiling was performed using RNA-seq from whole rosettes collected at 1 h, 3 h, 24 h, 72 h post-exposure. Analysis of gene expression was carried out comparing IR-exposed (10 cGy, 100 cGy) to mock-treated plants at each time point

低剂量电离辐射（low-dose ionizing radiation，IR）对植物的影响日益受到关注——此类辐射可能出现在太空飞行过程中，也可能源自人类活动（如核能发电），后者可能导致放射性物质向环境中释放。长期以来，高剂量电离辐射被用于诱导植物突变，以期为农业产业获得优良性状。然而，目前对于植物暴露于急性低剂量电离辐射后的响应机制尚缺乏深入了解。
本研究采用多组学方法，对拟南芥（Arabidopsis thaliana）暴露于低剂量电离辐射后的响应进行表征。我们优化了单模板甲基转移酶可及性实验方案（Methyltransferase Accessibility Protocol for individual templates，MAPit）以适配植物样本，借此可在暴露72小时后检测植物对急性低剂量电离辐射（10 cGy与100 cGy）的表观遗传响应；同时并行开展RNA测序，以分析暴露后1、3、24及72小时的转录组响应。
我们发现，即便低至10 cGy的电离辐射暴露，即可在拟南芥中引发强烈的遗传响应，该响应最早可在暴露后1小时被检测到。对上述响应的分析显示，基因表达、染色质可及性与DNA甲基化均呈现剂量依赖性变化，这些变化表明乙烯信号通路与非生物胁迫响应是电离辐射相关转录及表观遗传改变的潜在调控基础。此类变化可在暴露后72小时内被观测到，提示其在急性暴露结束后仍可长期维持。本研究结果表明，拟南芥可通过诱导并调控乙烯响应通路，对低剂量电离辐射产生协同的多模态响应。
实验设计：为探究低剂量电离辐射对拟南芥（Col-0生态型）基因表达的影响，研究人员将拟南芥种子播种于高压灭菌的土壤中，于4℃低温处理3天以促进整齐发芽（Zhou等，2017）。植株于短日照条件（8小时光照/16小时黑暗）、22℃环境下培养1周，随后将每株幼苗移栽至36孔托盘的单个孔穴中。待植株生长至第4周时，将其置于¹³⁷Cs辐照仪中，以每秒1.4 cGy的剂量率接受γ电离辐射照射。实验组植株分别接受7秒（等效剂量10 cGy）、71秒（等效剂量100 cGy）的辐照，对照组植株不接受辐照（0 cGy，即"Mock"对照）。研究人员于辐照后1、3、24、72小时采集完整莲座叶，通过RNA测序开展基因表达谱分析。基因表达分析通过在每个时间点对比电离辐射暴露组（10 cGy、100 cGy）与Mock对照组植株的转录组数据完成。