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5,596 results for “Epigenetics”
Epigenetic induction may speed up or slow down speciation with gene flow: code and data
<p>Speciation is less likely to occur when there is gene flow between nascent species. Natural selection can oppose gene flow and promote speciation if there is variation in ecological conditions among the nascent species' locations. Previous theory on ecological speciation with gene flow has focused primarily on the role of genetic variation in ecological traits, largely neglecting the role of non-genetic inheritance or transgenerational plasticity. <span>Here we present the simulation code and data from</span> models incorporating both genetic and epigenetic inheritance, the latter representing a form of non-genetic inheritance. We investigate the rate of speciation for a population that inhabits two patches, connected by migration, and find that adaptively-biased epigenetic induction can speed up or slow down speciation, depending on the form of the map from genotype and epigenotype to phenotype. While adaptively-relevant epigenetic variation can speed up speciation by reducing the fitness of migrants and hybrids, it can also slow down speciation. This latter effect occurs when the epialleles are able to achieve adaptation faster than the genetic alleles, thereby weakening selection on the latter.</p>
Epigenetic clock estimations in patients with isolated REM Sleep Behavior Disorder
<p>Isolated REM Sleep Behavior Disorder (iRBD) is the strongest prodromal marker for conversion to α-synucleinopathies. A continuum between aging and neurodegeneration has been proposed, but this hypothesis has not been tested in iRBD so far. Here we used epigenetic clocks, estimated from DNA methylation arrays using the DNA Methylation Age Calculator available at https://dnamage.genetics.ucla.edu/home, to measure biological aging in videopolysomnography-confirmed iRBD patients (iRBDs, n=28), videopolysomnography-negative controls (CTR_neg; n=57), and controls from the general population (CTR_pop; n=31)<strong>.</strong></p>
Dataset for: Conformational and Thermodynamic Differences Underlying Wild-type and Mutant YEATS Domain Specificity for Epigenetic Marks
<p>The set of molecular dynamics trajectories generated and analyzed in the paper "Conformational and Thermodynamic Differences Underlying Wild-type and Mutant YEATS Domain Specificity for Epigenetic Marks." <strong>Citations should refer directly to the manuscript. </strong> The preprint version is available at: https://doi.org/10.1101/2022.07.14.500085</p> <p>The uploaded zip file "trajectory_data.zip" contains trajectories for the (1) apo (2) h3k27ac and (3) h3k9ac systems. In each directory is a subdirectory corresponding to the wild-type, deletion, and insertion mutations. In each of those subdirectories are 10 XTC files, which correspond to the trajectories for the 10 different simulations performed for each system, along with an AMBER-formated PRMTOP file. Solvent molecules were removed from each file, and trajectories were strided such that there is one frame per 500 ps. </p>
Interplay between Genetics, Epigenetics & Exposures- Proposed Algorithm for Pediatric Cancer Development
Interplay between Genetics, Epigenetics & Exposures- Proposed Algorithm for Pediatric Cancer Development
Data from: Extensive epigenetic reprogramming during the life cycle of Marchantia polymorpha
<p>This GFF contains M. polymorpha genes (taken from the official release v3.1, Phytozome 11, phytozome.jgi.doe.gov) and transposable elements and repeats identified in the study (see Materials and Methods).</p>
Plasticity and associated epigenetic mechanisms play a role in thermal evolution during range expansion
<p>Due to global change many species are shifting their distribution and are thereby confronted with novel thermal conditions at the moving range edges. <span>Especially during the initial phases of exposure to a new environment, it has been hypothesized that plasticity and associated epigenetic mechanisms enable species to cope with environmental change.</span> We tested this idea by capitalizing on the well-documented southward range expansion of the damselfly Ischnura elegans from France into Spain where the species has invaded warmer regions in the 1950s in eastern Spain (old edge region) and in the 2010s in central Spain (new edge region). Using a common garden experiment at rearing temperatures matching the ancestral and invaded thermal regimes, we tested for evolutionary changes in (thermal plasticity in) larval life history and heat tolerance in these expansion zones. Through the use of de- and hypermethylating agents we tested whether epigenetic mechanisms play a role in enabling heat tolerance during expansion. We used the phenotype of the native sister species in Spain, I. graellsii, as proxy for the locally adapted phenotype. New edge populations converged towards the phenotype of the native species through plastic thermal responses in life history and heat tolerance while old edge populations (partly) constitutively evolved a faster life history and higher heat tolerance than the core populations, thereby matching the native species. Only the heat tolerance of new edge populations increased significantly when exposed to the hypermethylating agent. This suggests that the DNA methylation machinery is more amenable to perturbation at the new edge and shows it is able to play a role in achieving a higher heat tolerance. Our results show that both (evolved) plasticity as well as associated epigenetic mechanisms are initially important when facing new thermal regimes but that their importance diminishes with time.</p>
Assessing the links between pollinators and the genetic and epigenetic features of plant species with contrasting distribution ranges
<p>In flowering plants, pollinators contribute to gene flow while they also respond to variation in plant traits together determined by genetic, epigenetic and environmental sources of variation. Consequently, a correlation between abundance and diversity of pollinators and the genetic and epigenetic characteristics of plant populations such as diversity or distinctiveness is expected. However, no study has explored these long-term dimensions of plant-pollinator interactions. Mediterranean narrow endemics often exhibit unexpectedly high levels of population genetic and epigenetic diversity. We hypothesize that pollinators may contribute to explain this pattern. Specifically, given the higher sensitivity of small, isolated population to gene flow, we expect a stronger association of pollinators with population genetic and epigenetic variability in narrow endemics than in widely distributed congeners. We studied five pairs of congeneric plant species, consisting of one narrow endemic with a restricted distribution and one widespread congener, found in the Sierra de Cazorla mountains (SE Spain). We characterized the pollinators in up to three populations per species to estimate their diversity and visitation rates. Additionally, we calculated the genetic and epigenetic diversity and distinctiveness of each population using AFLP markers and methylation-sensitive AFLP markers (MSAP), respectively. We assessed the relationship between pollinator diversity and visitation rates. The diversity of pollinators did not vary according to the plant´s distribution range, but visitation rate was higher in widespread species. As predicted, only narrow endemics showed a significant association between pollinators and their population genetic and epigenetic characteristics. Specifically, higher pollinator diversity and visitation rates entailed higher population genetic diversity and lower epigenetic distinctiveness. This work shows the importance of investigating the relationship between pollinator diversity and population genetics and epigenetics to better understand the evolution of plant rarity.</p>
Dataset for Article - a role of epigenetic mechanisms in regulating female reproductive responses to temperature in a pest beetle
<p>This dataset contains data for analysis on a role of epigenetic mechanisms in regulating female reproductive responses to temperature in a pest beetle. Dataset contains raw gene expression data, methylation-ELISA data, MSRE data and life history data collected in laboratory conditions using the study system, <em>Callosobruchus maculatus</em>.</p>
CancerEpiSys – Integrative analysis of epigenetic networks that determine the chronic lymphocytic leukemia disease state
<p>A public repository of data processed for Mallm, Iskar, Ishaque et. al. 2018 Linking aberrant chromatin features in chronic lymphocytic leukemia to deregulated transcription factor networks</p> <p><strong>Website:</strong> http://www.cancerepisys.org/cancerepisys/index.html</p> <p><strong>Github:</strong> https://github.com/CancerEpiSys/Mallm-et-al-processing-scripts</p> <p><strong>Research mission</strong></p> <p><em>CancerEpiSys</em> is a BMBF funded research project with the <a href="http://www.bmbf.de/foerderungen/15063.php">CancerSys program</a> that dissects the epigenetic networks associated with chronic lymphocytic leukemia (CLL) to develop novel diagnostic and therapeutic approaches for the disease. It has been initiated based on the emerging view that signals encoded in the DNA sequence, epigenetic modifications (e.g. DNA methylation, post-translational histone modifications), non-coding RNAs and nucleosome positioning are not independently regulated properties. Rather, these chromatin features are governed by an interconnected network of molecular processes that determine the cellular gene expression program. Any errors that occur in the interplay of these factors can lead to aberrant gene regulation associated with cancer. To rationalize the mode of action of novel ‘epigenetic’ drugs in cancer therapy that change properties of this network, we will dissect experimentally and mathematically the interdependence of these processes, focusing on CLL.</p> <p>The main objectives of <em>CancerEpiSys</em> are: (i) deciphering the relation of DNA sequence, epigenetic modifications, nucleosome positioning and aberrant gene expression in CLL, (ii) the identification of epigenetic network morphologies that describe the response to the epigenetic drugs panobinostat and 3-deazaneplanocin (DZNep) that inhibit histone deacetylases and methyltransferases, (iii) the characterization of epigenetic markers and chromatin features of CLL patient subgroups, and (iv) the integration of results into an analysis scheme for the epigenetic aberrations most relevant for prognostication, prediction of treatment relapse and stratification of patients with respect to therapeutic options. Moreover, our results will inform novel therapeutic approaches that target gene-expression programs at the epigenetic level to sensitize cancer cells towards apoptosis and anti-growth signals.</p>
Decoding the Epigenetics and Chromatin Loop Dynamics of Androgen Receptor-Mediated Transcription
<p>This repository stores the datasets for the "Decoding the Dynamic Regulation and Chromatin Architecture of Androgen Receptor-mediated Gene Expression" paper.</p>
Epigenetic mechanisms of partial dosage compensation in an avian, female heterogametic system
The evolution of genetic sex determination is often accompanied by degradation of one of the proto sex chromosomes. Male heterogametic systems have evolved convergent, epigenetic mechanisms restoring the resulting imbalance in gene dosage between diploid autosomes (AA) and the hemizygous sex chromosome (X). Female heterogametic systems (AA<sub>f</sub> ZW<sub>f</sub>, AA<sub>m</sub> ZZ<sub>m</sub>) tend to only show partial dosage compensation (0.5 < Z<sub>f</sub>:AA<sub>f</sub> < 1) and dosage balance (0.5f:ZZ<sub>m</sub><1). The underlying mechanism remains largely elusive. Here, we quantified gene expression for a total of 15 male and female Eurasian crows (<em>Corvus (corone) spp</em>.) raised under common garden conditions. In addition, we characterized aspects of the regulatory landscape quantifying genome-wide ATAC-seq and 5mC methylation profiles. Partial dosage compensation was explained by female upregulation of Z-linked genes accompanied by increased chromatin accessibility on the female Z chromosome. 5mC methylation was strongly reduced in open chromatin-regions and GC islands and showed chromosome-, but no sex-specific variation. With the exception of the pseudo-autosomal region (PAR), female upregulation of gene expression was evenly spread across the Z chromosome without evidence for regional epigenetic regulation, as has for example been suggested for the male hypermethylated region (MHM) in chicken. Our results support the hypothesis that partial dosage compensation in female heterogametic systems is subject to chromosome-wide, epigenetic control mediated by differential chromatin accessibility between the sexes.
Phenotypic, genetic, and epigenetic data from 29 Serratia marcescens strains from an evolution experiment
<p>This dataset contains phenotypic, genetic, and epigenetic data from 29 <em>Serratia marcescens</em> strains from an evolution experiment. In a previous study (https://doi.org/10.1111/evo.12148), the bacterium <em>S. marcescens</em> was left to evolve from a common ancestor culture in replicated populations kept under different temperature regimes, and evolved clones were isolated and their phenotypes measured. Here, we randomly selected 28 evolved clones from this experiment, as well as the original reference strain, and used PacBio single molecule real-time (SMRT) sequencing to obtain genetic and epigenetic (N6-methyladenine modifications, m6A) data. The goal of our study was to obtain a detailed description of the methylation landscape of <em>S. marcescens</em> and to examine the potential contributions of genetic and epigenetic changes to phenotypic adaptation.</p>
Increased epigenetic diversity and transient epigenetic memory in response to salinity stress in Thlaspi arvense
<p>Epigenetic diversity could play an important role in adaptive evolution of organisms, especially for plant species occurring in new and stressful environments. Thlaspi arvense (pennycress), a valuable oilseed crop, is widespread in temperate regions of the northern hemisphere. In this study, we investigated the effect of salinity stress on the epigenetic variation of DNA methylation and epigenetic stress memory in pennycress using methylation-sensitive amplification polymorphism (MSAP) markers. We examined how the status of DNA methylation changes across individuals in response to salinity stress and whether such an effect of maternal stress could be transferred to offspring for one or two generations in non-stressed environments. Our results based on 306 epiloci indicated no consistent change of DNA methylation status in specific epiloci across individuals within the same conditions. In contrast, we found that the epigenetic diversity at population level increased significantly in response to the stimulation of salinity stress; and this "stimulation effect" could be transferred partially in the form of stress memory to at least two generations of offspring in non-stressed environments. In addition, we observed a parallel change in functionally important traits, i.e. phenotypic variation was significantly higher in plants grown under salinity stress compared with those of control groups. Taken together, our results provide novel clues for the increased spontaneous epimutation rate in response to stress in plants, of potential adaptive significance.</p>
Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures
<p>Imaging data related to the "Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures" manuscript</p>
Data from: Epigenetically distinct synaptic architecture in clonal compartments in the teleostean dorsal pallium
<p><span>The dorsal telencephalon (i.e. the pallium) exhibits high anatomical diversity across vertebrate classes. The non-mammalian dorsal pallium accommodates various compartmentalized structures among species.</span> <span>The developmental, functional and evolutional diversity of the dorsal pallium remain unillustrated. Here, we analyzed the structure and epigenetic landscapes of cell lineages in the telencephalon of medaka fish (<em>Oryzias latipes</em>) which possesses a clearly delineated dorsal pallium (Dd2). We found that pallial anatomical regions, including Dd2, are formed by mutually exclusive clonal units, and that each pallium compartment exhibits a distinct epigenetic landscape. In particular, Dd2 possesses a unique open chromatin pattern that preferentially targets synapse-related genes. Indeed, Dd2 shows a high density of synapses. Finally, we identified several transcription factors as candidate regulators. Taken together, we suggest cell lineages are the basic components for the functional regionalization in the pallial anatomical compartments, and that their changes has been the driving force for evolutionary diversity.</span></p>
Data for: Whole genome deconvolution unveils Alzheimer's resilient epigenetic signature
<p><span>Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) accurately depicts the chromatin regulatory state and altered mechanisms guiding gene expression in disease. However, bulk sequencing entangles information from different cell types and obscures cellular heterogeneity. To address this, </span><span>we developed Cellformer, a deep learning method that deconvolutes bulk ATAC-seq into cell type-specific expression across the whole genome. Cellformer enables cost-effective cell type-specific open chromatin profiling in large cohorts. Applied to 191 bulk samples from 3 brain regions, Cellformer identifies cell type-specific gene regulatory mechanisms involved in resilience to Alzheimer's disease, an uncommon group of cognitively healthy individuals that harbor a high pathological load of Alzheimer's disease. Cell type-resolved chromatin profiling unveils cell type-specific pathways and nominates potential epigenetic mediators underlying resilience that may illuminate therapeutic opportunities to limit the cognitive impact of the disease. Cellformer is freely available to facilitate future investigations using high-throughput bulk ATAC-seq data.</span></p>
Heatwave resilience of juvenile white sturgeon is associated with epigenetic and transcriptional alterations
<p>Heatwaves are increasing in frequency and severity, posing a significant threat to organisms globally. In aquatic environments, heatwaves are often associated with low environmental oxygen, which is a deadly combination for fish. However, surprisingly little is known about the capacity of fishes to withstand these interacting stressors. This issue is particularly critical for species of extreme conservation concern such as sturgeon. We assessed the tolerance of juvenile white sturgeon from an endangered population to heatwave exposure and investigated how this exposure affects tolerance to additional acute stressors. We measured whole-animal thermal and hypoxic performance and underlying epigenetic and transcriptional mechanisms. Sturgeon exposed to a simulated heatwave had increased thermal tolerance and exhibited complete compensation for the effects of acute hypoxia. These changes were associated with an increase in mRNA levels involved in thermal and hypoxic stress (hsp90a, hsp90b, hsp70 and hif1a) following these stressors. Global DNA methylation was sensitive to heatwave exposure and rapidly responded to acute thermal and hypoxia stress over the course of an hour. These data demonstrate that juvenile white sturgeon exhibit substantial resilience to heatwaves, associated with improved cross-tolerance to additional acute stressors and involving rapid responses in both epigenetic and transcriptional mechanisms.</p>
Epigenetic deregulation of IFN and WNT pathways in AT2 cells impairs alveolar regeneration (in COPD)
<h2>Data-sets</h2><p>RNAseq_CountTable.tsv: Raw count table from RNA-seq experiments</p><p>WGBS_MethylationTable.tsv: Total read coverage and number of methylated sites at CpG positions (reference genome: hg19) </p><h2>Abstract</h2><p>Chronic lung diseases, including chronic obstructive pulmonary disease (COPD), affect over 500 million people and are a leading cause of death worldwide. A common feature of both chronic and acute lung diseases is altered respiratory barrier integrity and impaired lung regeneration. We hypothesized that alveolar type 2 (AT2) cells, as alveolar epithelial progenitors, will carry molecular alterations that compromise alveolar regeneration in COPD. Sorted AT2 cells from ex-smokers with and without COPD at different disease stages were subjected to RNA sequencing and whole-genome bisulfite sequencing to generate unbiased transcriptome and DNA methylation maps of alveolar progenitors in the lung. Our analysis revealed genome-wide epigenetic changes in AT2 cells during COPD that were associated with global gene expression changes. Integrative data analysis uncovered a strong anti-correlation between gene expression and promoter methylation, suggesting that dysregulation of COPD-associated pathways in AT2 cells may be regulated by DNA methylation. Interferon (IFN) signaling was the top-upregulated pathway associated with the concomitant loss of promoter DNA methylation. Epigenetic regulation of the IFN pathway was validated in both global and targeted DNA demethylation assays in A549 cells. Notably, targeted DNA demethylation of IRF9 triggered upregulation of IFN signaling, mimicking the effects observed in COPD AT2 cells in the profiling data. Our findings suggest that COPD-triggered epigenetic alterations in AT2 cells impair internal regeneration programs in human lung parenchyma.</p>
Avelumab In Combination Regimens That Include An Immune Agonist, Epigenetic Modulator, CD20 Antagonist and/or Conventional Chemotherapy in Patients With Relapsed or Refractory Diffuse Large B-cell Lym
ClinicalTrials.gov study NCT02951156. IPD Sharing: YES. Countries: 8. Publications: 1.
Efficacy and Safety of Decitabine as Epigenetic Priming With Induction Chemotherapy in Pediatric Acute Myelogenous Leukemia (AML) Subjects
ClinicalTrials.gov study NCT01177540. IPD Sharing: Not stated. Countries: 3. Publications: 1.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.