Fluorescence anisotropy study of radiation-induced DNA damage clustering based on FRET

Akamatsu, Kensuke; Shikazono, Naoya; Saito, Takeshi

doi:10.1007/s00216-020-03082-w

Cited by 8 publications

(4 citation statements)

References 41 publications

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“…Therefore, the present results suggested that carbon ions induced denser ionization and DNA breakage along the path of the ion particles that could result in the generation of rearrangements irrespective of the water content. The complexity and proximity of DNA damage has been shown to increase as the LET increases ( Akamatsu et al., 2021 ), although the effect of water content remains unclear. In contrast, the difference in the ratio of Del (2–99 bp) between carbon ions and gamma rays observed with dry-seed irradiation was not evident with seedling irradiation ( Figure 4A ).…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of seed and seedling irradiation with gamma rays and carbon ions for mutation induction in Arabidopsis

2023

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The molecular nature of mutations induced by ionizing radiation and chemical mutagens in plants is becoming clearer owing to the availability of high-throughput DNA sequencing technology. However, few studies have compared the induced mutations between different radiation qualities and between different irradiated materials with the same analysis method. To compare mutation induction between dry-seeds and seedlings irradiated with carbon ions and gamma rays in Arabidopsis, in this study we detected the mutations induced by seedling irradiation with gamma rays and analyzed the data together with data previously obtained for the other irradiation treatments. Mutation frequency at the equivalent dose for survival reduction was higher with gamma rays than with carbon ions, and was higher with dry-seed irradiation than with seedling irradiation. Carbon ions induced a higher frequency of deletions (2−99 bp) than gamma rays in the case of dry-seed irradiation, but this difference was less evident in the case of seedling irradiation. This result supported the inference that dry-seed irradiation under a lower water content more clearly reflects the difference in radiation quality. However, the ratio of rearrangements (inversions, translocations, and deletions larger than 100 bp), which are considered to be derived from the rejoining of two distantly located DNA breaks, was significantly higher with carbon ions than gamma rays irrespective of the irradiated material. This finding suggested that high-linear energy transfer radiation induced closely located DNA damage, irrespective of the water content of the material, that could lead to the generation of rearrangements. Taken together, the results provide an overall picture of radiation-induced mutation in Arabidopsis and will be useful for selection of a suitable radiation treatment for mutagenesis.

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Section: Discussionmentioning

confidence: 99%

Comparative analysis of seed and seedling irradiation with gamma rays and carbon ions for mutation induction in Arabidopsis

2023

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“…Furthermore, using the same sample for both ATAC-se and RNA-seq enabled a more direct and accurate comparison of the two results. Previous radiation biology experiments have confirmed that radiation tends to damage DNA with dense structures and nucleic acid aggregates ( Banerjee et al, 2019 ; Akamatsu et al, 2021 ; Wang et al, 2021 ), Therefore, the results of ATAC sequencing provide a wealth of information for identifying regulatory mechanisms at the source. The combination of RNA sequencing and ATAC sequencing is a perfect approach to explore the interplay between DNA and RNA.…”

Section: Discussionmentioning

confidence: 99%

Integration of RNA-seq and ATAC-seq analyzes the effect of low dose neutron-γ radiation on gene expression of lymphocytes from oilfield logging workers

Li,

Gao,

Pan

et al. 2023

Front. Chem.

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Objective: Although radiation workers are exposed to much lower doses of neutron-γ rays than those suffered in nuclear explosions and accidents, it does not mean that their health is not affected by radiation. Lower doses of radiation do not always cause morphological aberrations in chromosomes, so more sophisticated tests must be sought to specific alterations in the exposed cells. Our goal was to characterize the specific gene expression in lymphocytes from logging workers who were continuously exposed to low doses of neutron-γ radiation. We hypothesized that the combination of cell type-specific transcriptomes and open chromatin profiles would identify lymphocyte-specific gene alterations induced by long-term radiation with low-dose neutron-γ-rays and discover new regulatory pathways and transcriptional regulatory elements.Methods: Lymphocytes were extracted from workers who have been occupationally exposed to neutron-γ and workers unexposed to radiation in the same company. mRNA-seq and ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) were performed, followed integrative analysis to identify specific gene regulatory regions induced by neutron-γ radiation. A qPCR assay was then performed to verify the downregulation of RNA coding for ribosomal proteins and flow cytometry was used to detect ribosomal protein expression and cell cycle alterations.Results: We identified transcripts that were specifically induced by neutron-γ radiation and discovered differential open chromatin regions that correlated with these gene activation patterns. Notably, we observed a downward trend in the expression of both differentially expressed genes and open chromatin peaks. Our most significant finding was that the differential peak upregulated in ATAC-seq, while the differential gene was downregulated in the ribosome pathway. We confirmed that neutron-γ radiation leads to transcriptional inhibition by analyzing the most enriched promoters, examining RPS18 and RPS27A expression by qPCR, and analyzing protein-protein interactions of the differential genes. Ribosomal protein expression and cell cycle were also affected by neutron-γ as detected by flow cytometry.Conclusion: We have comprehensively analyzed the genetic landscape of human lymphocytes based on chromatin accessibility and transcript levels, enabling the identification of novel neutron-γ induced signature genes not previously known. By comparing fine-mapping of open chromatin and RNA reads, we have determined that neutron-γ specifically leads to downregulation of genes in the ribosome pathway, with pseudogenes potentially playing a crucial role.

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“…For example, 4 MeV α-particles (LET 105 keV/μm) have been predicted to produce one five-lesion cluster, four two-lesion clusters, and eight isolated lesions in a DNA fragment [ 7 ]. The detection of clustered DNA damage has been reported in isolated DNA and in cells after exposure to ionizing radiation, including low-energy electrons, or even by H 2 O 2 -induced oxidative stress ([ 4 , 5 , 6 , 10 , 11 , 12 , 13 , 14 ], reviewed in [ 15 ]). High LET radiation, which induces clustered DNA damage at a much higher frequency than γ-rays, produces the exact same oxidatively damaged bases as γ-rays and with the same occurrence, only with a different distribution.…”

Section: Introductionmentioning

confidence: 99%

Dissecting Highly Mutagenic Processing of Complex Clustered DNA Damage in Yeast Saccharomyces cerevisiae

Kozmin

Éot-Houllier

Reynaud-Angelin

et al. 2021

Cells

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Clusters of DNA damage, also called multiply damaged sites (MDS), are a signature of ionizing radiation exposure. They are defined as two or more lesions within one or two helix turns, which are created by the passage of a single radiation track. It has been shown that the clustering of DNA damage compromises their repair. Unresolved repair may lead to the formation of double-strand breaks (DSB) or the induction of mutation. We engineered three complex MDS, comprised of oxidatively damaged bases and a one-nucleotide (1 nt) gap (or not), in order to investigate the processing and the outcome of these MDS in yeast Saccharomyces cerevisiae. Such MDS could be caused by high linear energy transfer (LET) radiation. Using a whole-cell extract, deficient (or not) in base excision repair (BER), and a plasmid-based assay, we investigated in vitro excision/incision at the damaged bases and the mutations generated at MDS in wild-type, BER, and translesion synthesis-deficient cells. The processing of the studied MDS did not give rise to DSB (previously published). Our major finding is the extremely high mutation frequency that occurs at the MDS. The proposed processing of MDS is rather complex, and it largely depends on the nature and the distribution of the damaged bases relative to the 1 nt gap. Our results emphasize the deleterious consequences of MDS in eukaryotic cells.

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Fluorescence anisotropy study of radiation-induced DNA damage clustering based on FRET

Cited by 8 publications

References 41 publications

Comparative analysis of seed and seedling irradiation with gamma rays and carbon ions for mutation induction in Arabidopsis

Comparative analysis of seed and seedling irradiation with gamma rays and carbon ions for mutation induction in Arabidopsis

Integration of RNA-seq and ATAC-seq analyzes the effect of low dose neutron-γ radiation on gene expression of lymphocytes from oilfield logging workers

Dissecting Highly Mutagenic Processing of Complex Clustered DNA Damage in Yeast Saccharomyces cerevisiae

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