Similar Datasets
Project description:Previous studies have shown that exposure to ionising radiation (IR) results in DNA methylation changes in plants. However, to the best of our knowledge, this phenomenon is yet to be studied across multiple generations. Furthermore, the exact role of these changes in the IR-induced plant response is still far from understood. Here, we study the effect of gamma radiation on DNA methylation and its effect across generations in young Arabidopsis plant. A multigenerational set-up was used in which three generations of seven-day old Arabidopsis thaliana plants were exposed to either of the different radiation treatments (30 mGy h-1, 60 mGy h-1, 110 mGy h-1, or 430 mGy h-1) or to natural background radiation (control condition) for 14 days. The parental generation consisted of previously non-exposed plants, whereas generation 1 and generation 2 plants had already received a similar irradiation in the previous one or two generations, respectively. Directly after exposure the entire methylomes were analysed with UPLC-MS to measure whole genome methylation levels. Whole genome bisulphite sequencing (WGBS) was used to identify differentially methylated regions (DMRs), including their methylation context in the three generations in three different radiation conditions (control, 30 mGy/h, and 110 mGy/h). Both intra- and intergenerational comparisons of the genes and transposable elements (TEs) associated with the DMRs were made across the gamma radiation exposure conditions. It was apparent that there was a higher number of changes in CpG methylation, whereas only limited changes in CHG methylation occurred and no changes in CHH methylation were observed. A clear increase in IR-induced DMRs was seen over the three generations that were exposed to the lowest dose rate, where Gen 2 had a markedly higher number of DMRs than the previous two generations (Parent and Gen 1). Counterintuitively, we did not see significant differences in the plants exposed to the higher dose rate. In addition, a large number of DMRs associated with TEs were found, the majority of them being hyper methylated, likely leading to more genetic stability. Next to that, a significant number of DMRs were associated with genes (either in their promoter associated region or gene body). A functional analysis of these genes (not included in with this data) showed an enrichment for genes related to development as well as various stress responses, including DNA repair, RNA splicing, and (a)biotic stress responses. These observations indicate a role of DNA methylation in the regulation of these genes in response to IR exposure and shows a possible role for epigenetics in adaptation to IR in plants.
2021-01-31 | GSE157965 | GEO
Project description:Eukaryotic genomes must maintain stable inheritance of epigenetic states. In plants, DNA methylation patterns are faithfully inherited over many generations but it is unknown how the dynamic activities of cytosine DNA methyltransferases and 5-methylcytosine DNA glycosylases, which remove 5-methylcytosine by base excision repair, interact to maintain epigenetic homeostasis. Here we show that a methylation-sensing gene regulatory circuit centered on a 5-methylcytosine DNA glycosylase gene is required for long-term epigenetic fidelity in Arabidopsis. Disrupting this circuit causes widespread methylation losses and abnormal phenotypes that progressively worsen over generations. In heterochromatin, these losses are counteracted such that methylation returns to a normal level over four generations. However, thousands of loci in euchromatin progressively lose DNA methylation between generations and remain unmethylated. We conclude that actively maintained equilibrium between methylation and demethylation activities is required to ensure long-term stable inheritance of epigenetic information.
2017-12-01 | GSE104240 | GEO
Project description:Understanding how novel complex traits originate is a foundational challenge in evolutionary biology. Yet how descent with modification in developmental evolution may lead to morphological innovation remains poorly understood. We investigated the origin of thoracic horns in scarabaeine beetles, one of the most dramatic classes of secondary sexual traits in the animal kingdom. We show that thoracic horns derive from bilateral source tissues, that diverse wing genes are functionally required for instructing this process, and that in the absence of Hox-input thoracic horn primordia transform to contribute to ectopic wings. Once induced, however, the transcriptional profile of thoracic horns diverges markedly from that of wings and other wing serial homologs. Our results provide evidence for the serial homology between thoracic horns and insects wings, and suggest that other insect innovations may similarly derive from wing serial homologs and the concomitant recruitment of diverse genes from outside a wing formation context.
2020-04-02 | GSE137455 | GEO
Project description:Maternal care is associated with long-term effects on behavior and epigenetic programming of the NR3C1 (GLUCOCORTICOID RECEPTOR) gene in the hippocampus of both rats and humans. However, epigenetic changes at a single gene promoter are unlikely to account for the range of responses to the early life environment and the persistent change in expression of hundreds of additional genes in adult rats in response to differences in maternal care. Here we show that natural variations in maternal care are associated with coordinate changes in DNA methylation, chromatin, and gene expression spanning over a hundred kilobase pairs in the hippocampus of adult rats. The offspring of high compared to low maternal care mothers show epigenetic changes in promoters, exons, and gene ends and higher transcriptional activity across many genes, suggesting that a broad epigenetic regulation of gene expression may form part of a coordinated response to early maternal care.
2011-03-09 | GSE20714 | GEO
Project description:Genome wide DNA methylation profiling of peripheral blood samples. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs. Samples included 63 of male samples,and 54 of female samples from peripheral leukocytes. All samples were healthy controls.
2016-03-01 | GSE67393 | GEO
Project description:Genome-wide DNA methylation analysis on PCOS using Illumina HumanMethylation 450K BeadChips in 30 PCOS patients and 30 healthy controls
2016-08-22 | GSE80468 | GEO
Project description:Cytosine DNA methylation regulates the expression of eukaryotic genes and transposable elements. Methylation is copied by DNA methyltransferases after DNA replication, which results in faithful transmission of methylation patterns during cell division and, at least in flowering plants, across generations. Trans-generational inheritance is mediated by a small group of cells that includes gametes and their progenitors. However, methylation is usually analyzed in somatic tissues that do not contribute to the next generation, and the mechanisms of trans-generational inheritance are inferred from such studies. To gain a better understanding of how DNA methylation is inherited, we analyzed purified Arabidopsis thaliana sperm and vegetative cells – the cell types that comprise pollen – with mutations in the DRM, CMT2 and CMT3 methyltransferases.
2016-12-13 | GSE87170 | GEO
Project description:Genome wide DNA methylation profiling of invasive breast cancer samples isolated from an ethnically diverse group of 80 patients in the Breast Cancer Care in Chicago (BCCC) study. DNA was extracted from formalin fixed, paraffin-embedded samples on 80 patients (21 White, 31 African-American, 23 Hispanic and 5 not reported) (training dataset) enrolled in the BCCC. Hormone receptor status was defined as negative if tumors were negative for both estrogen and progesterone (ER/PR) receptors (N=22/75). Formalin-fixed, paraffin-embedded (FFPE) tumor samples came from the Breast Cancer Care in Chicago (BCCC) study (Dookeran KA, Silva A, Warnecke RB, Rauscher GH: Race/ethnicity and disparities in mastectomy practice in the Breast Cancer Care in Chicago study. Ann Surg Oncol 2015, 22:66–74). Copies of pathology reports and the corresponding set of Hematoxylin and Eosin (H&E) stained slides were requested from the pathology department at each diagnosing institution, and a single pathologist selected tumor blocks representative of the tumor. Two recuts (at 4 µm each) were made from each selected block for H&E staining. The recuts were then examined in order to identify invasive components of the sample, and areas were marked according to tissue component. Cores of invasive tissue (2 mm in diameter) were obtained from the marked areas and DNA was extracted for the DNA methylation study.
2016-02-12 | GSE72110 | GEO
Project description:DNA methylation may be involved in development of type 1 diabetes (T1D), but previous epigenome-wide association studies were conducted among cases with clinically diagnosed diabetes. Using multiple pre-disease peripheral blood samples on the Illumina 450K and EPIC platforms, we investigated longitudinal methylation differences between 87 T1D cases and 87 controls from the prospective Diabetes Autoimmunity Study in the Young (DAISY) cohort. Change in methylation with age differed between cases and controls in 10 regions. Average longitudinal methylation differed between cases and controls at two genomic positions and 28 regions. Some methylation differences were detectable and consistent as early as birth, including before and after the onset of preclinical islet autoimmunity. Results map to transcription factors, other protein coding genes, and non-coding regions of the genome with regulatory potential. The identification of methylation differences that predate islet autoimmunity and clinical diagnosis may suggest a role for epigenetics in T1D pathogenesis.
2020-03-09 | GSE142512 | GEO
Project description:We analyzed DNA methylation alterations upon acquired Venetoclax resistance using 8 different cell line pairs
2023-11-22 | GSE166577 | GEO