Dataset Information

Chromatin states responsible for the regulation of differentially expressed genes under ⁶⁰Co~? ray radiation in rice.

ABSTRACT:

Background

The role of histone modifications in the DNA damage response has been extensively studied in non-plant systems, including mammals and yeast. However, there is a lack of detailed evidence showing how chromatin dynamics, either an individual mark or combined chromatin states, participate in regulating differentially expressed genes in the plant DNA damage response.

Results

In this study, we used RNA-seq and ChIP-seq to show that differentially expressed genes (DEGs), in response to ionizing radiation (IR), might be involved in different pathways responsible for the DNA damage response. Moreover, chromatin structures associated with promoters, exons and intergenic regions are significantly affected by IR. Most importantly, either an individual mark or a certain chromatin state was found to be highly correlated with the expression of up-regulated genes. In contrast, only the chromatin states, as opposed to any individual marks tested, are related to the expression of the down-regulated genes.

Conclusions

Our findings demonstrate that IR-related DEGs are modulated by distinct epigenetic mechanisms. Either chromatin states or distinct histone dynamics may act sequentially or in combination in regulating up-regulated genes, but the complex chromatin structure is mainly responsible for the expression of down-regulated genes. Thus, this study provides new insights into how up- and down-regulated genes are epigenetically regulated at the chromatin levels, thereby helping us to understand distinct epigenetic mechanisms that function in the plant DNA damage response.

SUBMITTER: Pan X

PROVIDER: S-EPMC5639768 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature

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Publications

Chromatin states responsible for the regulation of differentially expressed genes under <sup>60</sup>Co~γ ray radiation in rice.

Pan Xiucai X Fang Yuan Y Yang Xueming X Zheng Dongyang D Chen Lifen L Wang Lei L Xiao Jin J Wang Xiu-E XE Wang Kai K Cheng Zhukuan Z Yu Hengxiu H Zhang Wenli W

BMC genomics 20171012 1

<h4>Background</h4>The role of histone modifications in the DNA damage response has been extensively studied in non-plant systems, including mammals and yeast. However, there is a lack of detailed evidence showing how chromatin dynamics, either an individual mark or combined chromatin states, participate in regulating differentially expressed genes in the plant DNA damage response.<h4>Results</h4>In this study, we used RNA-seq and ChIP-seq to show that differentially expressed genes (DEGs), in r ...[more]

PMID: 29025389

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Project description:Background: Radiation exposure due to the detonation of an improvised nuclear device remains a major security concern. Radiation from such a device involves a combination of photons and neutrons. Although photons will make the greater contribution to the total dose, neutrons will certainly have an impact on the severity of the exposure as they have high relative biological effectiveness. Results: We investigated the gene expression signatures in the blood of mice exposed to 3 Gy x-rays, 0.75 Gy of neutrons, or to mixed field photon/neutron with the neutron fraction contributing 5%, 15%, or 25% of a total 3 Gy radiation dose. Gene ontology and pathway analysis revealed that genes involved in protein ubiquitination pathways were significantly overrepresented in all radiation doses and qualities. On the other hand, eukaryotic initiation factor 2 (EIF2) signaling pathway was identified as one of the top 10 ranked canonical pathways in neutron, but not pure x-ray, exposures. In addition, the related mTOR and regulation of EIF4/p70S6K pathways were also significantly underrepresented in the exposures with a neutron component, but not in x-ray radiation. The majority of the changed genes in these pathways belonged to the ribosome biogenesis and translation machinery and included several translation initiation factors (e.g. Eif2ak4, Eif3f), as well as 40S and 60S ribosomal subunits (e.g. Rsp19, Rpl19, Rpl27). Many of the differentially downregulated ribosomal genes (e.g. RPS19, RPS28) have been causally associated with human bone marrow failure syndromes and hematologic malignancies. We also observed downregulation of transfer RNA processes, in the neutron-only exposure (p < 0.005). Ingenuity Pathway Analysis (p < 0.05) of differentially expressed genes predicted significantly suppressed activity of the upstream regulators c-Myc and Mycn, transcription factors known to control ribosome biogenesis. Conclusions: We describe the gene expression profile of mouse blood following exposure to mixed field neutron/x-ray irradiation. We have discovered that pathways related to protein translation are significantly underrepresented in the exposures containing a neutron component. Our results highlight the significance of neutron exposures that even the smallest percentage can have profound biological effects that will affect medical management and treatment decisions in case of a radiological emergency.

Dataset Information

Chromatin states responsible for the regulation of differentially expressed genes under ⁶⁰Co~? ray radiation in rice.

Background

Results

Conclusions

Publications

Chromatin states responsible for the regulation of differentially expressed genes under <sup>60</sup>Co~γ ray radiation in rice.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

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Dataset Information

Chromatin states responsible for the regulation of differentially expressed genes under 60Co~? ray radiation in rice.

Background

Results

Conclusions

Publications

Chromatin states responsible for the regulation of differentially expressed genes under <sup>60</sup>Co~γ ray radiation in rice.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Chromatin states responsible for the regulation of differentially expressed genes under ⁶⁰Co~? ray radiation in rice.