Integrated analysis of diverse transcriptomic data from Arabidopsis reveals genetic markers that reliably and reproducibly respond to ionizing radiation

Studies focused on the responses of plants to ionizing radiation are becoming more important due to the increased need for radiation-induced mutations, post-harvest or phytosanitary irradiation treatment of plants, and environmental monitoring of radioactive sites. To elucidate the influence of ionizing radiation on genome-wide transcription in plants, we performed integrated analysis of diverse transcriptomic data from different Arabidopsis samples and at various time points after γ irradiation or H2O2 treatment. The expression levels of most of the differentially expressed genes (DEGs) that were induced or repressed after γ irradiation returned to baseline levels of transcription within 12 h, while some of these genes showed prolonged transcriptional changes. Expression of the DEGs did not correlate with genomic DNA methylation; however, there were substantial differences in DEG levels between the wild type and the cmt3-11 mutant, which has a defect in non-CG DNA methylation. Moreover, the proportion of the DEGs in common between 2 independent experiments using different batches of samples was only 12–18%. These results suggest that there is a diversity or randomness in radiation-induced physiological or phenotypic alterations. However, the results also indicated that 47 DEGs maintained a transcriptional change until 48 h, and 7 of them, until 16 d. Forty-five additional DEGs were found to be sustainably induced or repressed until 24 h after γ irradiation regardless of sample-to-sample variation or genotype, and 4 or 2 of them, until 5 d or 16 d, respectively. Therefore, we suggest that the 4 γ-ray-responsive genes that showed sustainable transcriptional changes until day 5 would be reliable and reproducible genetic markers when evaluating the responsiveness of plants to γ-rays.

► Great variability is found in different γ-ray-responsive transcriptome data
► The γ-ray-induced transcriptional changes do not correlate with DNA methylation.
► Reliable and reproducible genetic markers to γ-rays are suggested in Arabidopsis.