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. 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