Dataset Information

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.

SUBMITTER: Li S

PROVIDER: S-EPMC5359294 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Laser Irradiation-Induced DNA Methylation Changes Are Heritable and Accompanied with Transpositional Activation of <i>mPing</i> in Rice.

Li Siyuan S Xia Qiong Q Wang Fang F Yu Xiaoming X Ma Jian J Kou Hongping H Lin Xiuyun X Gao Xiang X Liu Bao B

Frontiers in plant science 20170321

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 Nd<sup>3+</sup>YAG laser irradiation. We found that all four methylation patterns at the 5'-CCGG sites that are anal ...[more]

PMID: 28377781

Similar Datasets

Project description:BACKGROUND: mPing is an endogenous MITE in the rice genome, which is quiescent under normal conditions but can be induced towards mobilization under various stresses. The cellular mechanism responsible for modulating the activity of mPing remains unknown. Cytosine methylation is a major epigenetic modification in most eukaryotes, and the primary function of which is to serve as a genome defense system including taming activity of transposable elements (TEs). Given that tissue-culture is capable of inducing both methylation alteration and mPing transposition in certain rice genotypes, it provides a tractable system to investigate the possible relationship between the two phenomena. RESULTS: mPing transposition and cytosine methylation alteration were measured in callus and regenerated plants in three rice (ssp. indica) genotypes, V14, V27 and R09. All three genotypes showed transposition of mPing, though at various frequencies. Cytosine methylation alteration occurred both at the mPing-flanks and at random loci sampled globally in callus and regenerated plants of all three genotypes. However, a sharp difference in the changing patterns was noted between the mPing-flanks and random genomic loci, with a particular type of methylation modification, i.e., CNG hypermethylation, occurred predominantly at the mPing-flanks. Pearson's test on pairwise correlations indicated that mPing activity is positively correlated with specific patterns of methylation alteration at random genomic loci, while the element's immobility is positively correlated with methylation levels of the mPing's 5'-flanks. Bisulfite sequencing of two mPing-containing loci showed that whereas for the immobile locus loss of CG methylation in the 5'-flank was accompanied by an increase in CHG methylation, together with an overall increase in methylation of all three types (CG, CHG and CHH) in the mPing-body region, for the active locus erasure of CG methylation in the 5'-flank was not followed by such a change. CONCLUSION: Our results documented that tissue culture-induced mPing activity in rice ssp. indica is correlated with alteration in cytosine methylation patterns at both random genomic loci and the elements' flanks, while the stability of mPing positively correlates with enhanced methylation levels of both the flanks and probably the elements per se. Thus, our results implicate a possible role of cytosine methylation in maintaining mPing stability under normal conditions, and in releasing the element's activity as a consequence of epigenetic perturbation in a locus-specific manner under certain stress conditions.

Project description:BackgroundEtoposide (epipodophyllotoxin) is a chemical commonly used as an anti-cancer drug which inhibits DNA synthesis by blocking topoisomerase II activity. Previous studies in animal cells have demonstrated that etoposide constitutes a genotoxic stress which may induce genomic instability including mobilization of normally quiescent transposable elements (TEs). However, it remained unknown whether similar genetically mutagenic effects could be imposed by etoposide in plant cells. Also, no information is available with regard to whether the drug may cause a perturbation of epigenetic stability in any organism.ResultsTo investigate whether etoposide could generate genetic and/or epigenetic instability in plant cells, we applied etoposide to germinating seeds of six cultivated rice (Oryza sativa L.) genotypes including both subspecies, japonica and indica. Based on the methylation-sensitive gel-blotting results, epigenetic changes in DNA methylation of three TEs (Tos17, Osr23 and Osr36) and two protein-encoding genes (Homeobox and CDPK-related genes) were detected in the etoposide-treated plants (S0 generation) in four of the six studied japonica cultivars, Nipponbare, RZ1, RZ2, and RZ35, but not in the rest japonica cultivar (Matsumae) and the indica cultivar (93-11). DNA methylation changes in the etoposide-treated S0 rice plants were validated by bisulfite sequencing at both of two analyzed loci (Tos17 and Osr36). Transpositional activity was tested for eight TEs endogenous to the rice genome in both the S0 plants and their selfed progenies (S1 and S2) of one of the cultivars, RZ1, which manifested heritable phenotypic variations. Results indicated that no transposition occurred in the etoposide-treated S0 plants for any of the TEs. Nonetheless, a MITE transposon, mPing, showed rampant mobilization in the S1 and S2 progenies descended from the drug-treated S0 plants.ConclusionsOur results demonstrate that etoposide imposes a similar genotoxic stress on plant cells as it does on animal and human cells, which may induce transgenerational genomic instability by instigating transpositional activation of otherwise dormant TEs. In addition, we show for the first time that etoposide may induce epigenetic instability in the form of altered DNA methylation patterns in eukaryotes. However, penetrance of the genotoxic effects of etoposide on plant cells, as being reflected as genetic and epigenetic instability, appears to be in a strictly genotype- and/or generation-dependent manner.

Project description:The optimal method for decontamination of implant surfaces for peri-implantitis treatment remains controversial. In recent years, erbium-doped yttrium aluminum garnet (Er:YAG) laser irradiation and implantoplasty (IP) (i.e. mechanical modification of the implant) have been reported to be effective in decontaminating implant surfaces during the surgical treatment. Also, a lack of adequate keratinized mucosa (KM) around the implant is known to be associated with more plaque accumulation, tissue inflammation, attachment loss, and mucosal recession, increasing the risk of peri-implantitis. Therefore, free gingival graft (FGG) has been recommended for gaining adequate KM around the implant. However, the necessity of acquiring KM for the treatment of peri-implantitis using FGG remains unclear. In this report, we applied the apically positioned flap (APF) as resective surgery for peri-implantitis treatment in conjunction with IP and Er:YAG laser irradiation to polish/clean the implant surface. Furthermore, FGG was conducted simultaneously to create additional KM, which increased the tissue stability and contributed to the positive results. The two patients were 64 and 63 years old with a history of periodontitis. The removal of granulation tissue and debridement of contaminated implant surfaces were performed with Er:YAG laser irradiation post flap elevation and then modified smooth surfaces mechanically using IP. Er:YAG laser irradiation was also utilized to remove the titanium particles. In addition, we performed FGG to increase the width of KM as a vestibuloplasty. Peri-implant tissue inflammation and progressive bone resorption were not observed, and both patients maintained good oral hygiene conditions until the 1-year follow-up appointment. Bacterial analysis via high-throughput sequencing revealed proportional decreases in bacteria associated with periodontitis (Porphyromonas, Treponema, and Fusobacterium). To the best of our knowledge, this study is the first to describe peri-implantitis management and bacterial change before and after procedures by resective surgery combined with IP and Er:YAG laser irradiation for peri-implantitis treatment, accompanied by FGG for increasing KM around the implants.

Dataset Information

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

Publications

Laser Irradiation-Induced DNA Methylation Changes Are Heritable and Accompanied with Transpositional Activation of <i>mPing</i> in Rice.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets