Similar Datasets
Project description:In this study we screened for changes of DNA methylation in response to X-irradiation in the lymphoblastoid cell line GM12878 and the primary lung fibroblast cell line IMR90. We employed methylated DNA-Immunoprecipitation in combination with genome wide and region specific DNA microarrays to identify preferences of radiation induced changes of methylation with respect to genomic and epigenomic characteristics.
2018-03-31 | GSE98307 | GEO
Project description:In this study we screened for changes of DNA methylation in response to X-irradiation in the lymphoblastoid cell line GM12878 and the primary lung fibroblast cell line IMR90. We employed methylated DNA-Immunoprecipitation in combination with genome wide and region specific DNA microarrays to identify preferences of radiation induced changes of methylation with respect to genomic and epigenomic characteristics.
2018-03-31 | GSE98305 | GEO
Project description:Regional preferences of DNA methylation changes in response to X-ray-irradiation
| PRJNA384635 | ENA
Project description:Epigenetic alterations may contribute to the generation of cancer cells in a multi-step process of tumorigenesis following irradiation of normal body cells. Primary human fibroblasts with intact cell cycle checkpoints were used as a model to test whether X-ray irradiation with 2 and 4 Gray induces direct epigenetic effects (within the first cell cycle) in the exposed cells. ELISA-based fluorometric assays were consistent with slightly reduced global DNA methylation and hydroxymethylation, however the observed between-group differences were usually not significant. Similarly, bisulfite pyrosequencing of interspersed LINE-1 repeats and centromeric α-satellite DNA did not detect significant methylation differences between irradiated and non-irradiated cultures. Methylation of interspersed ALU repeats appeared to be slightly increased (one percentage point; p = 0.01) at 6 h after irradiation with 4 Gy. Single-cell analysis showed comparable variations in repeat methylation among individual cells in both irradiated and control cultures. Radiation-induced changes in global repeat methylation, if any, were much smaller than methylation variation between different fibroblast strains. Interestingly, α-satellite DNA methylation positively correlated with gestational age. Finally, 450K methylation arrays mainly targeting genes and CpG islands were used for global DNA methylation analysis. There were no detectable methylation differences in genic (promoter, 5' UTR, first exon, gene body, 3' UTR) and intergenic regions between irradiated and control fibroblast cultures. Although we cannot exclude minor effects, i.e. on individual CpG sites, collectively our data suggest that global DNA methylation remains rather stable in irradiated normal body cells in the early phase of DNA damage response.
| S-EPMC5425224 | biostudies-literature
Project description:In this study we addressed the question whether changes of DNA hydroxymethylation after X-ray irradiation occur in a random fashion or if they show preferences for specific regions or features. We did not only focus on gene loci and promotor sights but also on gene body hydroxymethylation alterations and associated changes in gene expression. A more profound insight into hydroxymethylation characteristics triggered by radiation could provide clues to mechanisms and consequences of cellular response to irradiation including the immediate consequence of DNA strand breaks associated with active DNA demethylation as well as the long term risk of tumorigenesis or other associated diseases.
2019-01-29 | GSE111437 | GEO
Project description:A flexible fiberoptic bronchoscope was inserted trans-orally and advanced through the vocal cords of subjects. Brochoalveolar lavage (BAL) fluid was obtained from tertiary airways in the right upper and lower lobes. The BAL procedure was performed sequentially in the right upper lobe (RUL) and right lower lobe (RLL) with 20 ml of sterile saline followed by 10 ml of air and this was repeated for a total of 5 times per airway. BAL fluid was then filtered through 2-layer gauze, centrifuged, and washed twice in 0.9% NaCl. Cells were counted with a T10 automated cell counter. Cytospins were performed using a Shandon Cytospin 3 centrifuge. 75,000 cells resuspended in 200 l of 0.9% NaCl were loaded into a cytology funnel and centrifuged for 10 mins. Cells were allowed to air dry and processed for viewing via Hema 3 Stat pack. One pair of samples (GEO accessions GSM3610354 [H_1_RLL] and GSM3610362 [H_1_RUL]) from our previous publication, collected and measured in the same manner, was also included in our present analysis. DNA was extracted from lung macrophages via Qiagen DNeasy Blood and Tissue Kit. DNA was quantitated on a Qubit 3.0 Fluorometer. Bisulfite conversion of DNA was performed using the Zymo EZ DNA methylation kit. The Illumina MethylationEPIC array hybridization and scanning were performed at the University of Southern California Molecular Genomics Core.
2019-08-20 | GSE132547 | GEO
Project description:The present study evaluated the genome-wide methylation level of the medial basal hypothalamus using reduced representation bisulfite sequencing (RRBS) in female- and male-oriented rams.
2022-05-18 | GSE158287 | GEO
Project description:A number of pulmonary diseases occur with upper lobe predominance, including cystic fibrosis and smoking-related chronic obstructive pulmonary disease. In the healthy lung, several physiologic and metabolic factors exhibit disparity when comparing the upper lobe of the lung to lower lobe, including differences in oxygenation, ventilation, lymphatic flow, pH, and blood flow. In this study, we asked whether these regional differences in the lung are associated with DNA methylation changes in lung macrophages that could potentially lead to altered cell responsiveness upon subsequent environmental challenge. All analyses were performed using primary lung macrophages collected via bronchoalveolar lavage from healthy human subjects with normal pulmonary function. Epigenome-wide DNA methylation was examined via Infinium MethylationEPIC (850K) array and validated by targeted next-generation bisulfite sequencing. We observed 95 CpG loci with significant differential methylation in lung macrophages, comparing upper lobe to lower lobe (all false discovery rate < 0.05). Several of these genes, including CLIP4, HSH2D, NR4A1, SNX10, and TYK2, have been implicated as participants in inflammatory/immune-related biological processes. Functionally, we identified phenotypic differences in oxygen use, comparing upper versus lower lung macrophages. Our results support a hypothesis that epigenetic changes, specifically DNA methylation, at a multitude of gene loci in lung macrophages are associated with metabolic differences regionally in lung.
| S-EPMC6686200 | biostudies-literature
Project description:Ionizing radiation, released during accidents at nuclear power plants or after atomic bomb explosions, is a potentially serious health threat for the exposed human population. This type of high-energy radiation causes DNA damage including single- and double-strand breaks and induces chromosomal rearrangements and mutations, but it is not known if ionizing radiation directly induces changes in the epigenome of irradiated cells. We treated normal human fibroblasts and normal human bronchial epithelial cells with different doses of gamma-radiation emitted from a cesium 137 (137Cs) radiation source. After a recovery period, we analyzed global DNA methylation patterns in the irradiated and control cells using the methylated-CpG island recovery assay (MIRA) method in combination with high-resolution microarrays. Bioinformatics analysis revealed only a small number of potential methylation changes with low fold-difference ratios in the irradiated cells. These minor methylation differences seen on the microarrays could not be verified by COBRA (combined bisulfite restriction analysis) or bisulfite sequencing of selected target loci. Our study shows that acute gamma-radiation treatment of two types of human cells had no appreciable effect on DNA cytosine methylation patterns in exposed cells.
2012-11-29 | GSE39038 | GEO
Project description:Unprotected exposure to UVB radiation from the sun and the resulting DNA damage are thought to be responsible for physiological changes in the skin and for a variety of skin cancers, including basal cell and squamous cell carcinoma and malignant melanoma. Although the mutagenic effects of UVB have been well documented and studied mechanistically, there is only limited information as to whether UV light may also be responsible for inducing epigenetic changes in the genome of exposed cells. DNA methylation is a stable epigenetic modification involved in gene control. To study the effects of UVB radiation on DNA methylation, we repeatedly exposed normal human keratinocytes to a UVB light source. After a recovery period, we analyzed global DNA methylation patterns in the irradiated and control cells using the methylated-CpG island recovery assay (MIRA) method in combination with high-resolution microarrays. Bioinformatics analysis revealed only a limited number of possible differences between UVB-exposed and control cells. However, these minor apparent changes could not be independently confirmed by bisulfite sequencing-based approaches. This study reveals that UVB irradiation of keratinocytes has no recognizable global effect on DNA methylation patterns and suggests that changes in DNA methylation, as observed in skin cancers, are not immediate consequences of human exposure to solar UVB irradiation.
2013-01-30 | GSE42943 | GEO