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}NCBI GEO2026 · RNA sequencing · 18 samples
Methylation Mesa define functional regulatory elements for targeted gene activation [patients]DNA methylation regulates transcription, yet the demethylation of canonical elements like promoter CpG islands exhibits inconsistent correlations with gene activation. We hypothesized that causal regulatory elements are defined by biophysical hypersensitivity. Profiling 24 whole-genome bisulfite sequencing samples across diverse human and murine models, we identified Methylation Mesa, narrow (~45-
NCBI GEO2026 · RNA sequencing · 30 samples
Methylation Mesa define functional regulatory elements for targeted gene activation [cell lines]DNA methylation regulates transcription, yet the demethylation of canonical elements like promoter CpG islands exhibits inconsistent correlations with gene activation. We hypothesized that causal regulatory elements are defined by biophysical hypersensitivity. Profiling 24 whole-genome bisulfite sequencing samples across diverse human and murine models, we identified Methylation Mesa, narrow (~45-
NCBI GEO2026 · Methylation profiling by high throughput sequencing · 10 samples
Sublethal Fipronil and Cyfluthrin Exposure Induces Locus-Specific DNA Hypomethylation at Stress, Immune, and Xenobiotic-Response Genes in Adult ZebrafishAquatic organisms are exposed to pesticide residues that can lead to non-lethal molecular effects. This study investigated DNA methylation at toxicologically relevant loci in adult zebrafish. Fish were exposed to low and high concentrations of each compound for 7 days under semi-static conditions. We performed targeted bisulfite amplicon sequencing at six loci representing stress response (hsp70.1
NCBI GEO2026 · Methylation profiling by high throughput sequencing · 4 samples
Epigenetic Disordering Drives Stemness, Senescence Escape and Tumor Heterogeneity [WGBS]Tumor heterogeneity is the substrate for tumor evolution and the linchpin of treatment resistance. The widespread epigenome repatterning that characterizes most cancers can generate cells with diverse identities and malignant features; however, how this occurs is not known. We show that high levels of the epigenetic regulator and oncogene UHRF1 in zebrafish hepatocytes rapidly induce disordering o
NCBI GEO2026 · Methylation profiling by high throughput sequencing · 150 samples
Chemicals linked to lower IQ in children induce neurodevelopmentally relevant DNA methylation changes in rat pups and effects on learning and memory in adulthoodDevelopmental exposure to environmental chemicals is increasingly associated with impaired neurodevelopment, yet the underlying molecular mechanisms remain unclear. Epigenetic modifications, particularly DNA methylation, may, at least partly, mediate these effects. In this study, we aimed to determine whether developmental exposure to chemicals associated with lower IQ in children induces early li
NCBI GEO2026 · Methylation profiling by high throughput sequencing · 16 samples
Site-specific ribosomal RNA methylation regulates cell cycle progression through mitotic translation controlTranscriptome-wide detection of m5C modification in NSUN5-KO and control cells along the cell cycle.
NCBI GEO2026 · Methylation profiling by high throughput sequencing · 20 samples
Reprograming of Circadian Rhythms by Dietary Methionine Starvation [meRIP-seq]The circadian clock tightly interacts with cellular metabolism, and nutritional challenges can profoundly remodel its function. Dietary methionine restriction (MR) has been shown to improve metabolic health and extend lifespan. However, the effects of MR on the circadian clock and the underlying mechanisms have remained unclear. In this study, we discover that a methionine deprivation (MD) diet in
NCBI GEO2026 · RNA sequencing · 153 samples
Reprograming of Circadian Rhythms by Dietary Methionine StarvationThis SuperSeries is composed of the SubSeries listed below.
NCBI GEO2026 · Methylation profiling by high throughput sequencing · 12 samples
Multi-tissue whole-genome bisulfite sequencing DNA methylation profiling of red-spotted grouper (Epinephelus akaara)Red-spotted grouper (Epinephelus akaara) is a high-value marine aquaculture species in East and Southeast Asia, yet genome-wide epigenomic resources for it remain scarce. Here we report a multi-tissue DNA methylation dataset generated by whole-genome bisulfite sequencing of four tissues (intestine, kidney, liver and spleen) of adult farmed E. akaara, with three biological replicates per tissue and
NCBI GEO2026 · Methylation profiling by high throughput sequencing · 4 samples
Genome-wide RRBS methylation profiling identifies NLRP7 promoter hypermethylation associated with disease severity in epidermolysis bullosa simplex [tissue vs blood RRBS]Reduced representation bisulfite sequencing (RRBS) was performed to investigate DNA methylation profiles in patients with epidermolysis bullosa (EB) exhibiting variable disease severity. Differential methylation analysis identified a differentially methylated region within the NLRP7 promoter and first exon. The dataset provides genome-wide DNA methylation profiles generated from peripheral blood l
NCBI GEO2026 · Methylation profiling by high throughput sequencing · 74 samples
Single-cell DNA methylation sequencing reveals epigenetic alterations induced by bovine oocyte in vitro maturationOocyte in vitro maturation (IVM) is a key step for the in vitro production of bovine embryos. However, there is a concern that this process may induce suboptimal developmental competence of bovine oocytes including epigenetic alterations. Currently, epigenetic profile of bovine oocyte IVM is relatively limited and inconsistent, probably arising from differences in the detection approach and experi
NCBI GEO2026 · RNA sequencing · 51 samples
PITX2 missense coding variant expression in mice reveals direct function in atrial fibrillationThis SuperSeries is composed of the SubSeries listed below.
NCBI GEO2026 · RNA sequencing · 16 samples
Intrauterine growth restriction is associated with adaptive hematopoietic reprogramming and selective immune rewiring in monozygotic twinsPrenatal growth restriction is linked to adverse neonatal and long-term health outcomes, potentially mediated by altered fetal immune development, yet underlying epigenetic mechanisms remain incompletely understood. Monozygotic dichorionic-diamniotic twins with selective fetal growth restriction (sFGR) provide a unique human model to study environmentally driven programming independent of genetic
NCBI GEO2026 · Methylation profiling by high throughput sequencing · 34 samples
Apple Gala spore’s DNA methylation profiles contribution of genotype and environment distinctionWe were interested in the contribution of DNA methylation and in particular Differentially Methylated Region (DRM) to distinguish or in contrary find a common methylated profile between Gala apple sports and/or different orchard localization. To answer theses scientific issue, we explored several questions (1) Are there common and specific Differentially Methylated Regions (DMRs) for all six Gala
NCBI GEO2026 · Methylation profiling by high throughput sequencing · 9 samples
Human Primordial Germ Cell Heterogeneity in vitro is Associated with Distinctive Biological States [WGBS]Primordial germ cells (PGCs) exhibit molecular heterogeneity during development, but whether this reflects distinct biological states remains unclear. Using human PGC-like cells (hPGCLCs) in extended culture with dual fluorescent reporters for TFAP2C and DND1, we investigated the functional significance of DND1 expression heterogeneity. Single-cell RNA sequencing revealed DND1+ hPGCLCs are enriche
NCBI GEO2026 · Excel spreadsheet · 25 samples
Histone Variant H2A.J is an Epigenetic Regulator of Metastasis in Lung AdenocarcinomaMetastasis is a major contributor to poor patient survival in lung adenocarcinoma (LUAD); however, the underlying mechanisms remain incompletely understood. Unlike tumorigenesis-associated mutations, recurrent genetic alterations specifically linked to metastasis have not been identified, suggesting that epigenetic mechanisms may play a key role. In this study, we report that histone H2A variant H
NCBI GEO2026 · RNA sequencing · 242 samples
Major alleles of CDCA7α shape CG-methylation in Arabidopsis thalianaThis SuperSeries is composed of the SubSeries listed below.
NCBI GEO2026 · Excel spreadsheet · 14 samples
Epigenomic Landscape of Oak (Quercus robur) across Seasons and GenerationsIn this study, we present a comprehensive seasonal and generational analysis of the epigenomic landscape of Quercus robur. By integrating high-resolution WGBS data from mature trees across Spring, Summer, and Autumn, we uncovered a dynamic shift in DNA methylation throughout the growing season, with a pronounced increase in CHH context methylation from Spring to Autumn. Furthermore, seedlings deri
NCBI GEO2026 · Methylation profiling by high throughput sequencing · 6 samples
Left-Right Asymmetry in the Breast TME is Associated with Distinct Bioelectric and Epigenetic Tumor FeaturesThe tumor microenvironment (TME) plays a pivotal role in cancer progression. Here, we report a left-right (L-R) asymmetry in the breast TMEs. Bioinformatic analyses of RNASeq data and histological data from TCGA, revealed that R-sided tumors exhibit higher stromal content and are enriched in cancer-associated fibroblasts (CAFs). These differences were validated in paired L-R PDX and xenograft mode
NCBI GEO2026 · Methylation profiling by high throughput sequencing · 38 samples
Molecular mechanisms of promoter silencing by transcriptional readthrough [Mmachc promoter targeted bisulfite-seq]Transcriptional interference is the in cis suppression of one transcriptional process by another. To define the mechanisms by which transcriptional readthrough is converted into stable gene silencing, we develop a mouse cell line model of the epigenetic form of cobalamin C deficiency (epi-cblC) by deleting the Prdx1 intron 5 splice acceptor, thereby inducing antisense transcription across Mmachc.
NCBI GEO2026 · Methylation profiling by high throughput sequencing · 22 samples
Long-lived epigenetic states convert all-or-none single-cell responses to graded population responses in mammalian expression systemsQuantitatively relating transcription factor (TF) input to gene expression output is central to understanding mammalian gene regulation and essential for designing predictable synthetic expression systems. However, even minimal synthetic systems often exhibit unexplained behaviors. In a widely used inducible mammalian expression system, we show that transcriptional responses appear graded and sigm
NCBI GEO2026 · RNA sequencing · 58 samples
Molecular mechanisms of promoter silencing by transcriptional readthroughThis SuperSeries is composed of the SubSeries listed below.
NCBI GEO2026 · RNA sequencing · 36 samples
Reconstruction of ancestral plant genomes for inter-crop translational researchWe present Ancestral Genome Reconstruction (AGR), an exploratory framework for the automated inference of "paleogenomes" from large-scale comparative datasets. By analyzing 84 extant angiosperm species, we reconstructed 10 key ancestral angiosperm genomes millions of years old. These reconstructed ancestors were instrumental in (1) estimating when angiosperms emerged, when major botanical families
NCBI GEO2026 · Excel spreadsheet · 42 samples
Contrasting epigenetic dynamics in chromosome arms and pericentromeres during ROS1-induced plant immune memory [BiSulfite-seq]Induced resistance against (hemi-)biotrophic pathogens can be triggered in Arabidopsis by 17β-estradiol (E2)-dependent activation of ROS1 in plants carrying the XVE:ROS1-YFP transgene. Here, we characterise the genome-wide cytosine DNA methylation changes associated with the estbalishment of this ROS1-mediated resistance.
NCBI GEO2026 · Methylation profiling by high throughput sequencing · 4 samples
mTRACE: Modification-enabled Tracking of RNA-associated Cellular Events [ac4C-seq]The life cycle of RNA is orchestrated by a series of molecular events whose dynamic regulation is central to gene expression and cellular function. However, existing methods face limitations in continuously recording these events in living cells. Here we introduce mTRACE (Modification-enabled Tracking of RNA-associated Cellular Events), a molecular recording framework that leverages RNA modificati