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180 results for “epigenetic mechanisms”
Data to reproduce analysis in "Systematic analysis of transcriptional and epigenetic effects of genetic variation in Kupffer cells enables discrimination of cell intrinsic and environment-dependent mechanisms"
<p>Here you can find the datasets necessary to reproduce all analyses described in the Glass lab paper by <a href="https://www.biorxiv.org/content/10.1101/2022.09.22.509046v1">Bennett et al</a>. The python and R code for reproducing analysis and figures can be found on our linked <a href="https://github.com/HunterBennett/KupfferCell_NaturalGeneticVariation">github repository.</a></p> <p>Briefly, this paper explores the effect of natural genetic variation <em>in vivo</em>, using Kupffer cells as a model cell type. We collect and analyze transcriptional and epigenetic data (ATAC-seq, H3K27Ac ChIP-seq) to identify putative <em>trans</em> regulators driving differential gene expression across inbred strains of mice. Additionally, we provide evidence that <em>trans</em> effects control a majority of strain differential genes at homeostasis while <em>cis</em> effects dominate the transcriptional response to an external signal (lipopolysaccharide).</p> <p>References:</p> <p>Hunter Bennett, Ty D. Troutman, Enchen Zhou, Nathanael J. Spann, Verena M. Link, Jason S. Seidman, Christian K. Nickl, Yohei Abe, Mashito Sakai, Martina P. Pasillas, Justin M. Marlman, Carlos Guzman, Mojgan Hosseini, Bernd Schnabl, Christopher K. Glass bioRxiv 2022.09.22.509046; doi: <a href="https://doi.org/10.1101/2022.09.22.509046">https://doi.org/10.1101/2022.09.22.509046</a></p> <p> </p>
Supplementary Data for "Epigenetic mechanisms controlling human leukemia stem cells and therapy resistance"
<p><strong>We performed functional genomic profiling of diverse leukemias using label tracing techniques. We identified AML stem cell quiescence is defined by distinct promoter-centered chromatin and gene expression dynamics, and controlled by a novel transcription factor network, which is associated with disease persistence and chemotherapy resistance in multiple patients. </strong></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>
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>
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.
Epigenetic mechanisms of partial dosage compensation in an avian, female heterogametic system
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A potential role for epigenetic mechanisms enabling appropriate seasonal reproductive transitions of liver yolk-precursor production
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Plasticity and associated epigenetic mechanisms play a role in thermal evolution during range expansion
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Data from: Reprograming of epigenetic mechanisms controlling host insect immunity and development in response to egg-laying by a parasitoid wasp
<p>Parasitoids are insects that use other insects as hosts. They sabotage host cellular and humoral defenses to promote the survival of their offspring by injecting viruses and venoms along with their eggs. Many pathogens and parasites disrupt host epigenetic mechanisms to overcome immune system defenses, and we hypothesized that parasitoids may utilize the same strategy. We used the ichneumon wasp Pimpla turionellae as a model idiobiont parasitoid to test this hypothesis, with pupae of the greater wax moth Galleria mellonella as the host. We found that parasitoid infestation involves the suppression of host immunity-related effector genes and the modulation of host genes involved in developmental hormone signaling. The transcriptional reprogramming of host genes following the injection of parasitoid eggs was associated with changes in host epigenetic mechanisms. The introduction of parasitoids resulted in a transient decrease in host global DNA methylation and the modulation of acetylation ratios for specific histones. Genes encoding regulators of histone acetylation and deacetylation were mostly downregulated in the parasitized pupae, suggesting that parasitoids can suppress host transcription. We also detected a strong parasitoid-specific effect on host microRNAs regulating gene expression at the post-transcriptional level. Our data therefore support the hypothesis that parasitoids may favor the survival of their offspring by interfering with host epigenetic mechanisms to suppress the immune system and disrupt development.</p>
Dataset: lhp1 FLC-Venus time course imaging – Hybrid protein assembly-histone modification mechanism for PRC2-based epigenetic switching and memory
<p>The histone modification H3K27me3 plays a central role in Polycomb-mediated epigenetic silencing. H3K27me3 recruits and allosterically activates Polycomb Repressive Complex 2 (PRC2), which adds this modification to nearby histones, providing a read/write mechanism for inheritance through DNA replication. However, for some PRC2 targets, a purely histone-based system for epigenetic inheritance may be insufficient. We address this issue at the Polycomb target Flowering Locus C (FLC) in Arabidopsis thaliana, as a narrow nucleation region of only ~three nucleosomes within FLC mediates epigenetic state switching and subsequent memory over many cell cycles. To explain the memory's unexpected persistence, we introduce a mathematical model incorporating extra protein memory storage elements with positive feedback that persist at the locus through DNA replication, in addition to histone modifications. Our hybrid model explains many features of epigenetic switching/memory at FLC and encapsulates generic mechanisms that may be widely applicable.</p>
Epigenetic Mechanisms and Severe Obesity (Biological Tissue Collection)
ClinicalTrials.gov study NCT02663388. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Genetic and Epigenetic Mechanisms of Developing Gestational Diabetes Mellitus and Its Effects on the Fetus
ClinicalTrials.gov study NCT03610178. IPD Sharing: NO. Countries: 1. Publications: 1.
Dataset: lhp1 FLC-Venus time course imaging – Hybrid protein assembly-histone modification mechanism for PRC2-based epigenetic switching and memory
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Data from: Reprograming of epigenetic mechanisms controlling host insect immunity and development in response to egg-laying by a parasitoid wasp
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Data from: An antagonistic epigenetic mechanism regulating gene expression in pollen revealed through single-nucleus multiomics
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Raw data related to: Molecular Mechanisms Controlling Foxp3 Expression in Health and Autoimmunity: From Epigenetic to Post-translational Regulation.
<p><strong>Abstract</strong></p> <p>The discovery of the transcription factor Forkhead box-p3 (Foxp3) has shed fundamental insights into the understanding of the molecular determinants leading to generation and maintenance of T regulatory (Treg) cells, a cell population with a key immunoregulatory role. Work over the past few years has shown that fine-tuned transcriptional and epigenetic events are required to ensure stable expression of Foxp3 in Treg cells. The equilibrium between phenotypic plasticity and stability of Treg cells is controlled at the molecular level by networks of transcription factors that bind regulatory sequences, such as enhancers and promoters, to regulate Foxp3 expression. Recent reports have suggested that specific modifications of DNA and histones are required for the establishment of the chromatin structure in conventional CD4+ T (Tconv) cells for their future differentiation into the Treg cell lineage. In this review, we discuss the molecular events that control Foxp3 gene expression and address the associated alterations observed in human diseases. Also, we explore how Foxp3 influences the gene expression programs in Treg cells and how unique properties of Treg cell subsets are defined by other transcription factors.</p> <p> </p> <p><strong>Progetto giovani ricercatori</strong>[GR-2016-02363725] dal titolo: "Immune Tolerance, Metabolism and Multiple Sclerosis: Novel Molecular Tools to Monitor Disease Pathogenesis and Progression"</p> <p> </p> <p> </p> <p> </p>
Data from: Exposure to a competitive social environment activates an epigenetic mechanism that limits pheomelanin synthesis in zebra finches
Competitive environments promote high testosterone levels, oxidative stress and, consequently, impair cellular homeostasis. The regulation of genes involved in the synthesis of the pigment pheomelanin in melanocytes seems to help to maintain homeostasis against environmental oxidative stress. Here, we experimentally increased social interactions in some zebra finch Taeniopygia guttata males by keeping them in groups of six birds during feather growth, while others were kept alone, to test if melanocytes show epigenetic lability under a competitive social environment. As these changes may depend on the oxidative status, we administrated buthionine sulfoximine (BSO) to decrease the antioxidant capacity of some birds. The competitive environment downregulated a gene involved in pheomelanin synthesis (Slc7a11) by changing the level of DNA methylation in feather melanocytes. In other genes involved in pheomelanin synthesis (Slc45a2, MC1R and AGRP), DNA methylation was also affected, but no changes in expression were detected. The exposure to the competitive environment did not affect systemic oxidative stress and damage, indicating that a protective epigenetic mechanism that changes the expression of Slc7a11 may have been activated. However, no changes on the pigmentation phenotype of birds were found, likely due to the short duration or low intensity of the competitive environment. BSO treatment did not affect the epigenetic mechanism, suggesting that the antioxidant capacity of birds was high enough to deal with the competitive environment. An epigenetic mechanism limiting pheomelanin synthesis gets therefore activated under exposure to a competitive environment in male zebra finches, which may help avoiding damage caused by competitive interactions.
Data from: Effects of acclimation time and epigenetic mechanisms on growth of Neurospora in fluctuating environments
Reaction norms or tolerance curves have often been used to predict how organisms deal with fluctuating environments. A potential drawback is that reaction norms measured in different constant environments may not capture all aspects of organismal responses to fluctuating environments. We examined growth of the filamentous fungus Neurospora crassa in fluctuating temperatures and tested if growth in fluctuating temperatures can be explained simply by growth in different constant temperatures or if more complex models are needed. In addition, as previous studies on fluctuating environments have revealed that past temperatures that organisms have experienced can affect their response to current temperature, we tested the roles of different epigenetic mechanisms in response to fluctuating environments using different mutants. We found that growth of Neurospora can be predicted in fluctuating temperatures to some extent if acclimation times are taken into account in the model. Interestingly, while fluctuating environments have been linked with epigenetic responses we found only some evidence of involvement of epigenetic mechanisms on tolerating fluctuating temperatures. Mutants which lacked H3K4 or H3K36 methylation had slightly impaired response to temperature fluctuations, in addition the H3K4 methylation mutant and a mutant in the RNA interference pathway had altered acclimation times.
Data from: Exposure to a competitive social environment activates an epigenetic mechanism that limits pheomelanin synthesis in zebra finches
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Data from: Effects of acclimation time and epigenetic mechanisms on growth of Neurospora in fluctuating environments
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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.
International Brain Laboratory public data
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.
OpenNeuro
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.