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4,916 results for “DNA methylation”
A plant virus differentially alters DNA methylation in two cryptic species of a hemipteran vector
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DNA methylation associates with sex-specific effects of experimentally increased yolk testosterone in wild nestlings
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CALERIE trial molecular data summary: DNA methylation, mRNA, smRNA for blood, adipose, and muscle
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Age estimation of captive Asian elephants (Elephas maximus) based on DNA methylation: An exploratory analysis using methylation-sensitive high-resolution melting (MS-HRM)
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Data from: Developmental stress does not induce genome-wide DNA methylation changes in wild great tit (Parus major) nestlings
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Rearing environment affects the genetic architecture and plasticity of DNA methylation in Chinook salmon
<p>Genetic architecture and phenotypic plasticity are important considerations when studying trait variation within and among populations. Since environmental change can induce shifts in the genetic architecture and plasticity of traits, it is important to consider both genetic and environmental sources of phenotypic variation. While there is overwhelming evidence for environmental effects on phenotype, the underlying mechanisms are less clear. Variation in DNA methylation is a potential mechanism mediating environmental effects on phenotype due to its sensitivity to environmental stimuli, transgenerational inheritance, and influences on transcription. To characterize the effect of environment on methylation, we created two 6x6 (North Carolina II) Chinook salmon breeding crosses and reared the offspring in two environments: uniform hatchery tanks and semi-natural stream channels. We sampled the fish twice during development, at the alevin (larval) and fry (juvenile) stages. We measured DNA methylation at 13 genes using a PCR-based bisulfite sequencing protocol. The genetic architecture of DNA methylation differed between rearing environments, with greater additive and non-additive genetic variance in hatchery fish and greater maternal effects in semi-natural channel fish, though gene-specific variation was evident. We observed plasticity in methylation across all assayed genes, as well as gene-specific effects at two genes in alevin and six genes in fry, indicating developmental stage-specific effects of rearing environment on methylation. Characterizing genetic and environmental influences on methylation is critical for future studies on DNA methylation as a potential mechanism for acclimation and adaptation.</p>
Data from: Ocean acidification induces subtle shifts in gene expression and DNA methylation in mantle tissue of the Eastern oyster (Crassostrea virginica)
<p><b><span>Early evidence suggests that DNA methylation can mediate phenotypic responses of marine calcifying species to ocean acidification (OA). Few studies, however, have explicitly studied DNA methylation in calcifying tissues through time. Here, we examined the phenotypic and molecular responses in the extrapallial fluid and mantle (fluid and tissue at the calcification site) in adult eastern oyster (</span><span>Crassostrea virginica</span><span>) exposed to experimental OA over 80 days. Oysters were reared under three experimental </span><span>p</span><span>CO</span><span><span>2</span></span><span> treatments ('control', 580 μatm; 'moderate OA', 1000 μatm; 'high OA', 2800 μatm) and sampled at 6 time points (24 hours - 80 days). We found that high OA initially induced an increase in the pH of the extrapallial fluid (pH</span><span><span>EPF</span></span><span>) relative to the external seawater that peaked at day 9, but then diminished over time. Calcification rates were significantly lower in the high OA treatment compared to the other treatments. To explore how oysters regulate their extrapallial fluid, gene expression and DNA methylation were examined in the mantle-edge tissue of oysters from days 9 and 80 in the control and high OA treatments. Mantle tissue mounted a significant global molecular response (both in the transcriptome and methylome) to OA that shifted through time. Although we did not find individual genes that were significantly differentially expressed under OA, the pH</span><span><span>EPF</span></span><span> was significantly correlated with the eigengene expression of several co-expressed gene clusters. A small number of OA-induced differentially methylated loci were discovered, which corresponded with a weak association between OA-induced changes in genome-wide gene body DNA methylation and gene expression.</span><span> </span><span>Gene body methylation, however, was not significantly correlated with the eigengene expression of pH</span><span><span>EPF</span></span><span>-correlated gene clusters. These results suggest that OA induces a subtle response in a large number of genes in </span><span>C. virginica</span><span>, but also indicate that plasticity at the molecular level may be limited. Our study highlights the need to reassess our understanding of tissue-specific molecular responses in marine calcifiers</span><span>, </span><span>as well as the role of DNA methylation and gene expression in mediating physiological and biomineralization responses to OA. </span></b></p>
DNA methylation following long-term pulmonary multi-walled carbon nanotubes exposure in mice
<p>Whole Genome Bisulphite Sequencing (WGBS) experiment to assess DNA methylation patterns in mice lungs 56 days after exposure to Multi-Walled Carbon NanoTubes (MWCNTs). The doses of MWCNTs used in this experiment were 0, 40 or 80 μg/mouse. In this record, we provide WGBS coverage files along with bedgraph files.</p>
Data from: Developmental Dieldrin exposure alters DNA methylation at genes related to dopaminergic neuron development and Parkinson's disease in mouse midbrain
Human and animal studies have shown that exposure to the organochlorine pesticide dieldrin is associated with increased risk of Parkinson's disease (PD). Despite previous work showing a link between developmental dieldrin exposure and increased neuronal susceptibility to MPTP toxicity in male C57BL/6 mice, the mechanism mediating this effect has not been identified. Here, we tested the hypothesis that developmental exposure to dieldrin increases neuronal susceptibility via genome-wide changes in DNA methylation. Starting at 8 weeks of age and prior to mating, female C57BL/6 mice were exposed to 0.3 mg/kg dieldrin by feeding (every 3 days) throughout breeding, gestation, and lactation. At 12 weeks of age, pups were sacrificed and ventral mesencephalon, containing primarily substantia nigra, were microdissected. DNA was isolated and dieldrin-related changes in DNA methylation were assessed via reduced representation bisulfite sequencing (RRBS). We identified significant, sex-specific differentially methylated CpGs (DMCs) and regions (DMRs) by developmental dieldrin exposure (FDRNr4a2 and Lmx1b genes, which are involved in dopaminergic neuron development and maintenance. Developmental dieldrin exposure had distinct effects on the male and female epigenome. Together, our data suggest that developmental dieldrin exposure establishes sex-specific poised epigenetic states early in life. These poised epigenomes may mediate sensitivity to subsequent toxic stimuli and contribute to the development of late-life neurodegenerative disease, including PD.
Topological Overlap Matrices for DNA Methylation data of Gestational Diabetes Cohort with BMI and Exposure Status
<p>DNA methylation in placenta was measured with the Infinium HumanMethylation450 BeadChip (Illumina, Inc) microarray, in a sample of 28 women, 20 of whom had a gestational diabetes (GD)-affected pregnancy and 8 who did not. We used GD status as our exposure variable, assuming that this has widespread effects on DNA methylation and on its correlation patterns. Our response, Y, is the standardized body mass index (BMI) in the offspring at the age of 5. For the 10,000 most variable probes, we provide 3 topological overlap matrices (TOM), which are used in our analysis (note that each of the following TOM matrices are a 10,000 by 10,000 symmetric matrix with row names and column names corresponding to the CpG probe IDs:</p> <ol> <li>TOM_Methylation_All_10k.rds: based on all 28 subjects, </li> <li>TOM_Methylation_E0_10k.rds: based on the 8 subjects without a GD-affected pregnancy</li> <li>TOM_Methylation_E1_10k.rds: based on the 20 subjects with a GD-affected pregnancy </li> </ol> <p>The BMI (phenotype) and GD status (exposure) are given in the following dataset:</p> <ol> <li>BMI_and_Exposure_Status.rds: 28 x 2 matrix of the phenotype and exposure. each row is a subject.</li> </ol> <p>Using our ECLUST method (preprint available at http://sahirbhatnagar.com/slides/manuscript1_SB_v4.pdf), we derive 77 clusters, and here we provide the 1st principal component of each cluster:</p> <ol> <li>Cluster_Summary_1stPC.rds: 28 x 77 matrix, where each row is a subject, in the same order as the BMI_and_Exposure_Status.rds data</li> <li>Cluster_CpGs_names.rds: a list of length 77, where each element of the list contains the list of CpG probe IDs contained in each of the clusters</li> </ol> <p>To read in the data use the readRDS function, e.g.:</p> <p>TOM_All <- readRDS(file = "TOM_Methylation_All_10k.rds")</p>
Supplementary information associated with a "Whole-Organism Integrated DNA Methylation and Transcriptomics Analysis of Butterfly Metamorphosis".
<p>Supplementary information, annotation and code related to the manuscript studying <em>Bicyclus anynana</em> development entitled "Whole-Organism Integrated DNA Methylation and Transcriptomics Analysis of Butterfly Metamorphosis".</p>
Reciprocal expression of MADS-box genes and DNA methylation reconfiguration initiate bisexual cones in spruce
<p>The naturally occurring bisexual cone of gymnosperms is considered to have been a potential intermediate stage in the origin of flowers, but the mechanisms governing bisexual cone formation remain largely elusive. Here, we employed transcriptomic and DNA methylomic analyses, together with hormone measurement, to investigate the molecular mechanisms underlying bisexual cone development in a conifer species <em>Picea crassifolia</em>. Our study reveals a "bisexual" expression profile in bisexual cones, especially in expression patterns of B-, C-class and <em>LEAFY</em> genes, supporting the out of male model. <em>GGM7</em> could be essential for initiating bisexual cones. DNA methylation reconfiguration in bisexual cones affects the expression of genes crucial for cone development, including <em>PcDAL12</em>, <em>PcDAL10</em>, <em>PcNEEDLY</em> and <em>PcHDG5</em>. Auxin likely plays an important role in the development of female structures of bisexual cones. This study unveils the potential mechanisms responsible for bisexual cone formation in conifers and may shed light on the development of bisexuality.</p>
Data from: Avian offspring prenatal DNA methylation response to maternal corticosterone dosing during reproduction
<p>Avian embryos develop in an egg composition which reflects both maternal condition and the recent environment of their mother. In birds, yolk corticosterone (CORT) influences development by impacting pre- and postnatal growth, as well as nestling stress responses and development. One possible mechanism through which maternal CORT may affect offspring development is via changes to offspring DNA methylation. We sought to investigate this, for the first time in birds, by quantifying the impact of manipulations to maternal CORT on offspring DNA methylation. We non-invasively manipulated plasma CORT concentrations of egg-laying female zebra finches (<em>Taeniopygia </em><em>castanotis</em>) with an acute dose of CORT administered around the time of ovulation and collected their eggs. We then assessed DNA methylation in the resulting embryonic tissue and in their associated vitelline membrane blood vessels, during early development (5 days after lay), using two established methods - liquid chromatography–mass spectrometry (LC-MS) and methylation-sensitive amplification fragment length polymorphism (MS-AFLP). LC-MS analysis showed that global DNA methylation was lower in embryos from CORT-treated mothers, compared to control embryos. In contrast, blood vessel DNA from eggs from CORT-treated mothers showed global methylation increases, compared to control samples. There was a higher proportion of global DNA methylation in the embryonic DNA of second clutches, compared to first clutches. Locus-specific analyses using MS-AFLP did not reveal a treatment effect. Our results indicate that an acute elevation of maternal CORT around ovulation impacts DNA methylation patterns in their offspring. This could provide a mechanistic understanding of how a mother's experience can affect her offspring's phenotype.</p>
Blood DNA Methylation Profiling Identifies Cathepsin Z Dysregulation in Pulmonary Arterial Hypertension
<p>Ulrich, A., Wu, Y., Draisma, H., Wharton, J., Swietlik, E. M., Cebola, I., Vasilaki, E., Balkhiyarova, Z., Jarvelin, M. R., Auvinen, J., Herzig, K. H., Coghlan, J. G., Lordan, J., Church, C., Howard, L. S., Pepke-Zaba, J., Toshner, M., Wort, S. J., Kiely, D. G., Condliffe, R., … Rhodes, C. J. (2024). <a href="https://pubmed.ncbi.nlm.nih.gov/38184627/"><strong>Blood DNA methylation profiling identifies cathepsin Z dysregulation in pulmonary arterial hypertension</strong></a>. <em>Nature communications</em>, <em>15</em>(1), 330. https://doi.org/10.1038/s41467-023-44683-0</p> <p>Maternal educational attainment (MEA) shapes offspring health through multiple potential pathways. Differential DNA methylation may provide a mechanistic understanding of these long-term associations. We aimed to quantify the associations of MEA with offspring DNA methylation levels at birth, in childhood and in adolescence. Using 37 studies from high-income countries, we performed meta-analysis of epigenome-wide association studies (EWAS) to quantify the associations of completed years of MEA at the time of pregnancy with offspring DNA methylation levels at birth (n = 9 881), in childhood (n = 2 017), and adolescence (n = 2 740), adjusting for relevant covariates. MEA was found to be associated with DNA methylation at 473 cytosine-phosphate-guanine sites at birth, one in childhood, and four in adolescence. We observed enrichment for findings from previous EWAS on maternal folate, vitamin-B12 concentrations, maternal smoking, and pre-pregnancy BMI. The associations were directionally consistent with MEA being inversely associated with behaviours including smoking and BMI. Our findings form a bridge between socio-economic factors and biology and highlight potential pathways underlying effects of maternal education. The results broaden our understanding of bio-social associations linked to differential DNA methylation in multiple early stages of life. The data generated also offers an important resource to help a more precise understanding of the social determinants of health.</p>
Methylation and gene expression data from: Differential DNA methylation across environments has no effect on gene expression in the eastern oyster
<p>1. It has been hypothesized that environmentally induced changes to gene body methylation could facilitate adaptive transgenerational responses to changing environments.</p> <p>2. We compared patterns of global gene expression (Tag-seq) and gene body methylation (reduced representation bisulfite sequencing) in 80 eastern oysters (<i>Crassostrea virginica</i>) from six full-sib families, common gardened for 14 months at two sites in the northern Gulf of Mexico that differed in mean salinity.</p> <p>3. At the time of sampling, oysters from the two sites differed in mass by 60% and in parasite loads by nearly two orders of magnitude. They also differentially expressed 35% of measured transcripts. However, we observed differential methylation at only 1.4% of potentially methylated loci in comparisons between individuals from these different environments, and little correspondence between differential methylation and differential gene expression.</p> <p>4. Instead, methylation patterns were largely driven by genetic differences among families, with a PERMANOVA analysis indicating nearly a two orders of magnitude greater number of genes differentially methylated between families than between environments.</p> <p>5. An analysis of CpG observed/expected values (CpG O/E ) across the <i>C. virginica</i> genome showed a distinct bimodal distribution, with genes from the first cluster showing the lower CpG O/E values, greater methylation, and higher, and more stable gene expression, while genes from the second cluster showed lower methylation, and lower and more variable gene expression.</p> <p>6. Taken together, the differential methylation results suggest that only a small portion of the <i>C. virginica</i> genome is affected by environmentally induced changes in methylation. At this point, there is little evidence to suggest that environmentally induced methylation states would play a leading role in regulating gene expression responses to new environments.</p>
Supplementary materials for "Integration of public DNA methylation and expression networks via eQTMs improves prediction of functional gene–gene associations"
<p>This repository contained supplementary materials in the study named: "<strong>Integration of public DNA methylation and expression networks via eQTMs improves prediction of functional gene–gene associations.</strong>"</p> <p>For extracting all files from the downloaded tar.gz file, the following commanda could be used:</p> <pre><code>tar -xf supplementary_materials.tar.gz </code></pre> <p>The supplementary_materials/data diretcory contains the following sections:</p> <p></p> <ol> <li>eqtm_predictions: This contains the training and testing datasets for the eQTM prediction procedures</li> <li>public_methylation_data_and_pca: This contains the harmonized public DNA methylation dataset and its first 100 PCA components</li> <li>cca_data: This contains the CCA components for the public DNA methylation and gene expression datasets for the negative eQTMs, and the input datasets for the functional gene pair prediction analylsis.</li> <li>gene_enrichment_results_for_cca: This contains the gene enrichment results for the CCA components for negative and positive eQTMs</li> </ol> <p>The supplementary_materials/model directory contains the following sections:</p> <ol> <li>disease_tissue_predictions: This contains the models trained for tissue prediction and disease prediction based on the PCA components from the public DNA methylation data</li> <li>eqtm_predictions: This contains models trained for eQTM prediction</li> <li>cca_transformations: This contains CCA transformation models and models for STRING gene pair predictions </li> </ol>
Data from: Inheritance of DNA methylation differences in the mangrove Rhizophora mangle
<p>This record contains supplementary information for the article "Inheritance of DNA methylation differences in the mangrove Rhizophora mangle" published in Evolution&Development. It contains the barcodes (barcodes.txt), the reference contigs (contigs.fasta.gz), the annotation of the reference contigs (mergedAnnot.csv.gz), the SNPs (snps.vcf.gz), the methylation data (methylation.txt.gz), and the experimental design (design.txt). All data are unfiltered. Short reads are available on SRA (PRJNA746695). Note that demultiplexing of the pooled reads (SRX11452376) will fail because the barcodes are already removed and the header information is lost during SRA submission. Instead, use the pre-demultiplexed reads that are as well linked to PRJNA746695.</p> <p><br> </p> <p><strong>Table S13 (TableS13_DSSwithGeneAnnotation.offspringFams.csv.gz): </strong></p> <p>Differential cytosine methylation between families using the mother data set. The first three columns fragment number ("chr"), the position within the fragment ("pos"), and the sequence context ("context"). Columns with the pattern FDR_<X>_vs_<Y> contain false discovery rates of a test comparing population X with population Y. Average DNA methylation levels for each population are given in the columns "AC", "FD", "HI", "UTB", "WB", and "WI". The remaining columns contain the annotation of the fragment, for example whether it matches to a gene and if yes, the gene name ID and description are provided.</p>
Maternal Mediterranean diet in pregnancy and newborn DNA methylation: a meta-analysis in the PACE Consortium
<p>Higher adherence to the Mediterranean diet during pregnancy may be related to offspring cord blood DNA methylation. In a meta-analysis of epigenome-wide association studies (EWAS) in 2802 mother-child pairs from 5 cohorts we calculated the relative Mediterranean diet (rMED) score and an adjusted rMED excluding alcohol (rMEDp). rMEDp was associated with cord blood DNA methylation at cg23757341.</p>
Maternal Glycemic Dysregulation During Pregnancy and Neonatal Blood DNA Methylation: Meta-analyses of Epigenome-Wide Association Studies
<p>Maternal glycemic dysregulation during pregnancy increases the risk of adverse health outcomes in her offspring, a risk thought to be linearly related to maternal hyperglycemia. It is hypothesized that changes in offspring DNA methylation (DNAm) underline these associations. To address this hypothesis, we conducted fixed-effects meta-analyses of epigenome-wide association study (EWAS) results from eight birth cohorts investigating relationships between cord blood DNAm and fetal exposure to maternal glucose (Nmaximum= 3,503), insulin (Nmaximum= 2,062), and area under the curve of glucose (AUCgluc) following oral glucose tolerance tests (Nmaximum = 1,505). Inflation and bias was addressed with the bacon Bioconductor package for individual cohorts and the meta-analysis results and reported model estimates and standard errors are adjusted. Greater maternal AUCgluc during pregnancy was associated with lower cord blood DNAm at neighboring CpGs cg26974062 and cg02988288 in TXNIP. Follow-up analyses show that these changes may have functional and later-life consequences and warrant further mediation and causal analysis. </p> <p>The corresponding paper can be found here: https://doi.org/10.2337/dc21-1701.</p> <p>Upload of this dataset was completed by The EWAS Catalog team. The data can be queried along with hundreds of other EWAS at ewascatalog.org. To upload your EWAS summary statistics and have a Zenodo DOI generated for you go to ewascatalog.org/upload.</p>
Genome-wide DNA methylation profiling identifies epigenetic signatures of β-lactams induced fatal anaphylactic shock
<p>Drug hypersensitivity is one of the most frequent causes of anaphylaxis in adults, of which antibiotics are the most common culprits, particularly β-lactams induced anaphylactic shock deaths. We provided the genome wide DNA methylation profiling study of PBMC from 14 individuals peripheral venous blood samples. Illumina Infinium Human Methylation EPIC BeadChip was used. Among the 14 individuals, 8 patients were died from β-lactams induced anaphylactic shock, 6 healthy individuals were controls. Inclusion criteria for the β-lactams induced anaphylactic shock as follows: ①A clear history of β-lactams transfusion or components of β-lactams detected from blood (or skin of suspicious infusion site); ②Shock symptoms occurred after infusion of β-lactams and died within a short period of time; ③The immunohistochemical results of throat, lung and gastrointestinal tissues showed that tryptase or chymase were mostly positive expression; ④ Excluding other causes (disease, poisoning) of death; ⑤ No decay occurred in the corpse.Inclusion criteria for controls as follows: ① Healthy, no previous common underlying diseases and no history of genetic disease; ② No history of allergies to drugs, food, pollen and so on; ③Skin prick test (SPT) is negative, allergen-specific IgE (sIgE)< 100IU/mL; the skin test results of β-lactam drugs were negative.</p>
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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)
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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.