Global methylation in Arabidopsis plants after multigenerational exposure to high temperatures
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE173660 | GEO | 2021/05/01
REPOSITORIES: GEO
Similar Datasets
Project description:Global methylation in Arabidopsis plants after multigenerational exposure to high temperatures
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Project description:Transcriptional profiling of two-old week pfd4/Col-0 (WT) plants in response to low temperatures
2017-12-01 | GSE90746 | GEO
Project description:BackgroundElevated temperatures can cause physiological, biochemical, and molecular responses in plants that can greatly affect their growth and development. Mutations are the most fundamental force driving biological evolution. However, how long-term elevations in temperature influence the accumulation of mutations in plants remains unknown.ResultsMultigenerational exposure of Arabidopsis MA (mutation accumulation) lines and MA populations to extreme heat and moderate warming results in significantly increased mutation rates in single-nucleotide variants (SNVs) and small indels. We observe distinctive mutational spectra under extreme and moderately elevated temperatures, with significant increases in transition and transversion frequencies. Mutation occurs more frequently in intergenic regions, coding regions, and transposable elements in plants grown under elevated temperatures. At elevated temperatures, more mutations accumulate in genes associated with defense responses, DNA repair, and signaling. Notably, the distribution patterns of mutations among all progeny differ between MA populations and MA lines, suggesting that stronger selection effects occurred in populations. Methylation is observed more frequently at mutation sites, indicating its contribution to the mutation process at elevated temperatures. Mutations occurring within the same genome under elevated temperatures are significantly biased toward low gene density regions, special trinucleotides, tandem repeats, and adjacent simple repeats. Additionally, mutations found in all progeny overlap significantly with genetic variations reported in 1001 Genomes, suggesting non-uniform distribution of de novo mutations through the genome.ConclusionCollectively, our results suggest that elevated temperatures can accelerate the accumulation, and alter the molecular profiles, of DNA mutations in plants, thus providing significant insight into how environmental temperatures fuel plant evolution.
| S-EPMC8145854 | biostudies-literature
Project description:This research uses consecutive generations of two independent mutation accumulation (MA) lines in model organism A. thaliana to understand transgenerational stability of epialleles via self-fertilization. With whole-genome bisulfite sequencing, regions of instability were identified and quantified. The vast majority of the methylated genome is stably inherited to offspring and the identified unstable regions do not change frequently between generations. Additionally, an epigenetic cross of two MA lines was created to understand inheritance patterns of epialleles via outcrossing in the absence of genetic variation. Whole-genome bisulfite sequencing was used to predict epigenotype of the offspring without single nucleotide polymorphisms. In regions of differential methylation between the parents, about half of regions show predictable inheritance.
2017-07-24 | GSE94298 | GEO
Project description:The notion that genes are the sole units of heredity and that a barrier exists between soma and germline has been a major hurdle in elucidating the heritability of traits that were observed to follow a non-Mendelian inheritance pattern. It was only after the conception of “epigenetics” by C. H. Waddington that the effect of parental environment on subsequent generations via non-DNA sequence-based mechanisms, such as DNA methylation, chromatin modifications, non-coding RNAs and proteins, could be established in various organisms, now referred to as multigenerational epigenetic inheritance. Despite the growing body of evidence, the male gamete-derived epigenetic factors that mediate the transmission of such phenotypes are seldom explored, particularly in the model organism Drosophila melanogaster. Using the heat stress-induced multigenerational epigenetic inheritance paradigm in a widely used position-effect variegation line of Drosophila, named white-mottled, we have dissected the effect of heat stress on the sperm proteome in the current study. We demonstrate that multiple successive generations of heat stress at the early embryonic stage results in a significant downregulation of proteins associated with translation, chromatin organization, microtubule-based processes, and generation of metabolites and energy in the Drosophila sperms. Based on our findings, we propose chromatin-based epigenetic mechanisms, a well-established mechanism for environmentally induced multigenerational effects, as a plausible way of transmitting heat stress memory via the male germ line in subsequent generations. Moreover, we demonstrate the effect of multiple generations of heat stress on the reproductive fitness of Drosophila, shedding light on the adaptive or maladaptive potential of heat stress-induced multigenerational phenotypes.
2024-05-10 | PXD037488 | Pride
Project description:The conventional view is that high temperatures cause microorganisms to replicate slowly or die. In this view, microorganisms autonomously combat heat-induced damage. However, microorganisms co-exist with each other, which raises the underexplored and timely question of whether microorganisms can cooperatively combat heat-induced damages at high temperatures. Here, we use the budding yeast Saccharomyces cerevisiae to show that cells can help each other and their future generations to survive and replicate at high temperatures. As a consequence, even at the same temperature, a yeast population can exponentially grow, never grow or grow after unpredictable durations (hours to days) of stasis, depending on its population density. Through the same mechanism, yeasts collectively delay and can eventually stop their approach to extinction, with higher population densities stopping faster. These features arise from yeasts secreting and extracellularly accumulating glutathione—a ubiquitous heat-damage-preventing antioxidant. We show that the secretion of glutathione, which eliminates harmful extracellular chemicals, is both necessary and sufficient for yeasts to collectively survive at high temperatures. A mathematical model, which is generally applicable to any cells that cooperatively replicate by secreting molecules, recapitulates all of these features. Our study demonstrates how organisms can cooperatively define and extend the boundaries of life-permitting temperatures.
2020-03-24 | GSE137151 | GEO
Project description:Exposure to TCDD early in development produces reproductive abnormalities and decreased reproductive capacity in males in subsequent generations. We used WGBS to investigate differential methylation in testicular tissue and identified distinct multigenerational and transgenerational methylation changes due to legacy TCDD exposure in males.
2022-04-20 | GSE149919 | GEO
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:45 genome-wide microarray measurements for 23 mutation accumulation lines grown in YPD liquid culture MA lines obtained by single-colony transfer on YPD plates for 600 generations, starting from a BY4741 derived strain (see Zeyl C, DeVisser JA: Estimates of the rate and distribution of fitness effects of spontaneous mutation in Saccharomyces cerevisiae. Genetics 2001, 157:53–61)
2010-10-19 | GSE24770 | GEO
Project description:ChIP-seq for PIF4-HA plants under different temperatures.
| PRJNA1013083 | ENA