Genetic Consequences of Acute/Chronic Gamma and Carbon Ion Irradiation of Arabidopsis thaliana

Hase, Yoshihiro; Satoh, Katsuya; Seito, Hajime; Oono, Yutaka

doi:10.3389/fpls.2020.00336

Cited by 46 publications

(94 citation statements)

References 29 publications

(48 reference statements)

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“…In the human genome, the mean Ti/Tv ratio is approximately 2.1, while we calculated a mean Ti/Tv ratio of 1.45 for IR-induced SNVs across all samples. This is in line with different studies in plants and mammals [32,33], who report a conspicuously high proportion of transversions after irradiation. Moreover, it is consistent with our observations in exome data from HGF cells that received an identical treatment as the cells used in this study [34].…”

Section: Mutational Signatures On a Genomic Levelsupporting

confidence: 92%

Genome-Wide DNA Alterations in X-Irradiated Human Gingiva Fibroblasts

Nath

Hagenau

Weiß

et al. 2020

IJMS

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While ionizing radiation (IR) is a powerful tool in medical diagnostics, nuclear medicine, and radiology, it also is a serious threat to the integrity of genetic material. Mutagenic effects of IR to the human genome have long been the subject of research, yet still comparatively little is known about the genome-wide effects of IR exposure on the DNA-sequence level. In this study, we employed high throughput sequencing technologies to investigate IR-induced DNA alterations in human gingiva fibroblasts (HGF) that were acutely exposed to 0.5, 2, and 10 Gy of 240 kV X-radiation followed by repair times of 16 h or 7 days before whole-genome sequencing (WGS). Our analysis of the obtained WGS datasets revealed patterns of IR-induced variant (SNV and InDel) accumulation across the genome, within chromosomes as well as around the borders of topologically associating domains (TADs). Chromosome 19 consistently accumulated the highest SNVs and InDels events. Translocations showed variable patterns but with recurrent chromosomes of origin (e.g., Chr7 and Chr16). IR-induced InDels showed a relative increase in number relative to SNVs and a characteristic signature with respect to the frequency of triplet deletions in areas without repetitive or microhomology features. Overall experimental conditions and datasets the majority of SNVs per genome had no or little predicted functional impact with a maximum of 62, showing damaging potential. A dose-dependent effect of IR was surprisingly not apparent. We also observed a significant reduction in transition/transversion (Ti/Tv) ratios for IR-dependent SNVs, which could point to a contribution of the mismatch repair (MMR) system that strongly favors the repair of transitions over transversions, to the IR-induced DNA-damage response in human cells. Taken together, our results show the presence of distinguishable characteristic patterns of IR-induced DNA-alterations on a genome-wide level and implicate DNA-repair mechanisms in the formation of these signatures.

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Section: Mutational Signatures On a Genomic Levelsupporting

confidence: 92%

Genome-Wide DNA Alterations in X-Irradiated Human Gingiva Fibroblasts

Nath

Hagenau

Weiß

et al. 2020

IJMS

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“…The AtKu70 −/− mutant appeared to be more sensitive than the AtLig4 −/− mutant, with a significantly lower survival rate at 250 and 300 Gy ( t -test, P < 0.05). Both mutant lines were treated with 100 Gy and then compared with the previously reported wild-type plants gamma-irradiated with 1000 Gy [ 24 ]. These doses correspond to ~50% Dq for each material.…”

Section: Resultsmentioning

confidence: 99%

“…Seedlings with more than five fresh and viable rosette leaves (true leaves) were counted as survivors. Survival curves were drawn based on the single hit-multitarget theory as previously described [ 24 ]. The M 2 seeds were harvested from individual plants.…”

Section: Methodsmentioning

confidence: 99%

“…The raw sequence reads were processed and mapped to the Arabidopsis reference genome (TAIR10), and candidate mutation sites were identified using GATK Haplotype Caller (version 3.4, https://software.broadinstitute.org/gatk/ ), Pindel (version 0.2.4, http://gmt.genome.wustl.edu/packages/pindel/user-manual.html ) and BreakDancer (version 1.4.5, http://breakdancer.sourceforge.net/ ) algorithms as previously described [ 24 ]. All mutations assayed are in unique regions, since we used the golden path of chromosomes 1–5 (119, 146, 348 bp) as a reference sequence, which does not contain redundant regions.…”

Section: Methodsmentioning

confidence: 99%

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Characterization of gamma irradiation-induced mutations in Arabidopsis mutants deficient in non-homologous end joining

Hase

Satoh

et al. 2020

Journal of Radiation Research

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To investigate the involvement of the non-homologous end joining (NHEJ) pathway in plant mutagenesis by ionizing radiation, we conducted a genome-wide characterization of the mutations induced by gamma rays in NHEJ-deficient Arabidopsis mutants (AtKu70−/− and AtLig4−/−). Although both mutants were more sensitive to gamma rays than the wild-type control, the AtKu70−/− mutant was slightly more sensitive than the AtLig4−/− mutant. Single-base substitutions (SBSs) were the predominant mutations in the wild-type control, whereas deletions (≥2 bp) and complex-type mutations [i.e. more than two SBSs or short insertion and deletions (InDels) separated by fewer than 10 bp] were frequently induced in the mutants. Single-base deletions were the most frequent deletions in the wild-type control, whereas the most common deletions in the mutants were 11–30 bp. The apparent microhomology at the rejoined sites of deletions peaked at 2 bp in the wild-type control, but was 3–4 bp in the mutants. This suggests the involvement of alternative end joining and single-strand annealing pathways involving increased microhomology for rejoining DNA ends. Complex-type mutations comprising short InDels were frequently detected in the mutants, but not in the wild-type control. Accordingly, NHEJ is more precise than the backup pathways, and is the main pathway for rejoining the broken DNA ends induced by ionizing radiation in plants.

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“…Diverse cultivars of T. aestivum have been obtained by hybridization, genetic modification, or mutation so as to improve crop productivity and quality. In mutation breeding, mutagens, such as chemical (i.e., ethyl methanesulphonate and methylnitrosourea), physical (i.e., ultraviolet lights, gamma-rays, and proton beams), or combined mutagens, have been used for developing cultivars with novel mutational characteristics, while preserving the unique and excellent properties of the plant [20][21][22]. More than 2500 mutant varieties have been developed via physical mutagen treatment and have been registered with the Food and Agriculture Organization/International Atomic Energy Agency (FAO/IAEA) [23].…”

Section: Introductionmentioning

confidence: 99%

Comparison of Flavonoid Profiles in Sprouts of Radiation Breeding Wheat Lines (Triticum aestivum L.)

et al. 2020

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Wheat (Triticum aestivum Linn.; Poaceae), one of the most popular food crops worldwide, contains basic and essential nutrients and various health benefiting phytochemicals. Among them, flavonoids have attracted significant interest owing to their various health-promoting properties. In this study, 35 wheat mutant lines were developed via gamma-irradiated mutation breeding from the original cultivar. The effects of radiation breeding on the endogenous phytochemical production in the sprouts of these mutant lines were investigated using high performance liquid chromatography-diode array detector-electrospray ionization mass spectrometry (HPLC-DAD-ESIMS) with multivariate analysis for the first time in this study. Fourteen characteristic peaks, including eleven flavone C-glycosides, two flavone O-glycosides, and one flavone, were identified. In addition, the contents of three flavone C-glycosides, namely, isoschaftoside, isoorientin, and isoscoparin, in 37 wheat sprout samples from the original cultivar, certificated cultivar, and the mutant lines were determined. A heat map combined with hierarchical clustering showed variation in the relative content for the flavonoids between the 37 wheat sprout samples, clustering into three groups. On principal component analysis scores scatter and loading plots, significant differences in the levels of flavonoids were found between the samples and several markers responsible for group separation were detected. These results provide a scientific reference for the phytochemical variation in wheat mutant lines, thereby aiding in further mutation mechanism studies and for the quality control of the improved wheat cultivars.

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Genetic Consequences of Acute/Chronic Gamma and Carbon Ion Irradiation of Arabidopsis thaliana

Cited by 46 publications

References 29 publications

Genome-Wide DNA Alterations in X-Irradiated Human Gingiva Fibroblasts

Genome-Wide DNA Alterations in X-Irradiated Human Gingiva Fibroblasts

Characterization of gamma irradiation-induced mutations in Arabidopsis mutants deficient in non-homologous end joining

Comparison of Flavonoid Profiles in Sprouts of Radiation Breeding Wheat Lines (Triticum aestivum L.)

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