Laser Irradiation-Induced DNA Methylation Changes Are Heritable and Accompanied with Transpositional Activation of mPing in Rice

Abstract

DNA methylation is an integral component of the epigenetic code in most higher eukaryotes. Exploring the extent to which DNA methylation can be altered under a specific condition and its heritability is important for elucidating the biological functions of this epigenetic modification. Here, we conducted MSAP analysis of rice plants with altered phenotypes subsequent to a low-dose Nd3+YAG laser irradiation. We found that all four methylation patterns at the 5′-CCGG sites that are analyzable by MSAP showed substantial changes in the immediately treated M0 plants. Interestingly, the frequencies of hypo- and hypermethylation were of similar extents, which largely offset each other and render the total methylation levels unchanged. Further analysis revealed that the altered methylation patterns were meiotically heritable to at least the M2 generation but accompanied with further changes in each generation. The methylation changes and their heritability of the metastable epigenetic state were verified by bisulfite sequencing of portion of the retrotranspon, Tos17, an established locus for assessing DNA methylation liability in rice. Real-time PCR assay indicated that the expression of various methylation-related chromatin genes was perturbed, and a Pearson correlation analysis showed that many of these genes, especially two AGOs (AGO4-1 and AGO4-2), were significantly correlated with the methylation pattern alterations. In addition, excisions of a MITE transposon, mPing, occurred rampantly in the laser irradiated plants and their progenies. Together, our results indicate that heritable DNA methylation changes can be readily induced by low-dose laser irradiation, and which can be accompanied by transpostional activation of transposable elements.

The impact of transposable elements on the structure, evolution and function of the rice genome

“…These are three retrotransposons – Tos17 ( Hirochika et al ., ) , Lullaby (Picault et al ., ) and Karma (Komatsu et al ., ) – that can be activated during callus vitro culture. Additionally, the transposon nDart can be activated when rice plants are treated with methylation inhibitor (Eun et al ., ), and mPing can be activated using laser irradiation (S. Li et al ., ). To date, there is no other TE family among the hundreds that the rice genome harbours for which such direct evidence of activity has been established.…”

RNA directed DNA methylation and seed plant genome evolution

“…c Response to biotic and abiotic stress utilizes RNA directed DNA methylation by altering epigenetic marks and creating epialleles which may be heritable to progeny as a result of epigenetic heritability Similar to biotic stress, several crop plants as well as the model A. thaliana have been analyzed for potential methylation roles in conditions of high ultraviolet rays, nutrient deficiency, heat (Hashida et al 2006), cold, drought, among other abiotic stresses and illustrated variation in global or specific locus methylation (Bucher et al 2011). These variations occurred possibly for transcriptional regulation of abiotic stress genes (Narsai et al 2017;Li et al 2017). In some instances these changes in the epigenome are stably inherited to the next generation (Thiebaut et al 2019;Martienssen and Colot 2001).…”

Bioaugmentation of Vibrio alginolyticus in phytoremediation of aluminium-contaminated soil using Scirpus grossus and Thypa angustifolia

“…Such finding was attributed to the toxicity of Al, which impeded the plant growth ( Setiadi and Anira, 2015 ). The presence of Al causes root damage, thereby inhibiting the absorption of water and minerals required by plants ( Bojórquez-Quintal et al., 2017 ). The height of T. angustifolia showed a fluctuating increase in the concentration of 0–500 mg/kg Al.…”