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187 results for “Maternal gene”
Data from: Phylogenetic conflict between species tree and maternally inherited gene trees in a clade of Emberiza buntings (Aves: Emberizidae)
<p>Different genomic regions may reflect conflicting phylogenetic topologies on account of incomplete lineage sorting and/or gene flow. Genomic data are necessary to reconstruct the true species tree and explore potential causes of phylogenetic conflict. Here, we investigate the phylogenetic relationships of four <em>Emberiza</em> species (Aves: Emberizidae) and discuss the potential causes of the observed mitochondrial non-monophyly of <em>Emberiza godlewskii</em> (Godlewski's bunting) using phylogenomic analyses based on whole genome resequencing data from 41 birds. Phylogenetic analyses based on both the whole mitochondrial genome and ~39 kilobases from the non-recombining W chromosome reveal that the northern and southern populations of <em>E. godlewskii</em> are each sister to <em>E. cioides</em> and <em>E. cia</em>, respectively. In contrast, phylogenetic analysis based on genome-wide data support the monophyly of <em>E. godlewskii</em> with the following tree topology: (((<em>E. godlewskii</em>, <em>E. cia</em>), <em>E. cioides</em>), <em>E. jankowskii</em>).<em> </em>Using D-statistics, we detected multiple gene flow events among different lineages, indicating pervasive introgressive hybridization within this clade. Introgression from an unsampled lineage that is sister to <em>E. cioides</em> or introgression from an unsampled mitochondrial + W chromosomal lineage of <em>E. cioides</em> into northern <em>E. godlewskii </em>may explain the phylogenetic conflict between the species tree estimated from genome-wide data and mtDNA/W trees. These results underscore the importance of using genomic data for phylogenetic reconstruction and species delimitation.</p>
Comparative Analysis of Maternal Gene Expression Patterns: Unraveling Evolutionary Signatures Across Reproductive Modes
<p>Dataset used to reproduce the analysis performed in "Comparative Analysis of Maternal Gene Expression Patterns: Unraveling Evolutionary Signatures Across Reproductive Modes" publication. The directory structure is the following:</p> <ul> <li>Gene_models - directory containing gene models (.gtf or .gff3 files) used for feature length comparisons across species</li> <li>intermediate_data - directory containing intermediate results from various scripts, the main purpose is to speed up the reproducibility of some longer running scripts <ul> <li>batch_adjusted_normalised_gene_expression_matrix.tsv - gene expression matrix used for evolutionary model fitting</li> <li>fc.tsv - fold change matrix used for evolutionary model fitting</li> <li>dated_species_tree.tre - species tree used throughout the model fitting step (newick format)</li> <li>DGE_script_enviorment.RData - saved R environment from differential gene expression analysis</li> <li>downregulated_IDs.RDS - gene IDs which undergo down-regulation throughout maternal-to-zygotic transition</li> <li>maternal_IDs.RDS - gene IDs which meet the cut-off criteria for being considered as maternally expressed</li> <li>N0_blasted.tsv - orthogroup annotations through blasting to a sequence database</li> <li>N0.tsv - orthogroups inferred from OrthoFinder</li> <li>OG_categories.tsv - classification of orthogroups based on them (I) having genes with maternal expression, but no significant down regulation, (II) having genes with maternal expression and significant down regulation throughout maternal-to-zygotic transition or (III) no maternal expression</li> <li>OG_presence.tsv - binary matrix coding for which orthogroup which species have gene expression values</li> <li>Paralog_variances.tsv - matrix containing variance metrics for paralogs in each species from before normalization across species</li> </ul> </li> <li>Pannzer2_annotation - directory containing GO annotations for all species from the Pannzer2 tool, used for GO analyses</li> <li>quantification_files - directory containing all salmon quantification outputs</li> <li>transcriptomes - <em>de novo</em> assembled transcriptomes for non-model species</li> </ul>
Data from: Phylogenetic conflict between species tree and maternally inherited gene trees in a clade of Emberiza buntings (Aves: Emberizidae)
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Data from: Impact on offspring methylation patterns of maternal gestational diabetes mellitus and intrauterine growth restraint suggest common genes and pathways linked to subsequent type 2 diabetes risk
Size at birth, postnatal weight gain, and adult risk for type 2 diabetes may reflect environmental exposures during developmental plasticity and may be mediated by epigenetics. Both low birth weight (BW), as a marker of fetal growth restraint, and high birth weight (BW), especially after gestational diabetes mellitus (GDM), have been linked to increased risk of adult type 2 diabetes. We assessed DNA methylation patterns using a bead chip in cord blood samples from infants of mothers with GDM (group 1) and infants with prenatal growth restraint indicated by rapid postnatal catch-up growth (group 2), compared with infants with normal postnatal growth (group 3). Seventy-five CpG loci were differentially methylated in groups 1 and 2 compared with the controls (group 3), representing 72 genes, many relevant to growth and diabetes. In replication studies using similar methodology, many of these differentially methylated regions were associated with levels of maternal glucose exposure below that defined by GDM [the Hyperglycemia and Adverse Pregnancy Outcome (HAPO) study] or were identified as changes observed after randomized periconceptional nutritional supplementation in a Gambian cohort characterized by maternal deprivation. These studies provide support for the concept that similar epigenetic modifications may underpin different prenatal exposures and potentially increase long-term risk for diseases such as type 2 diabetes.
The prenatal hypoxic pathology associated with maternal stress predisposes to dysregulated expression of the chrna7 gene and the subsequent development of nicotine addiction in adult offspring (Supplementary)
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Maternal glycemia in pregnancy is longitudinally associated with blood DNAm variation at the FSD1L gene from birth to 5 years of age
<p>Taschereau, A., Thibeault, K., Allard, C., Juvinao-Quintero, D., Perron, P., Lutz, S. M., Bouchard, L., & Hivert, M. F. (2023). Maternal glycemia in pregnancy is longitudinally associated with blood DNAm variation at the FSD1L gene from birth to 5 years of age. Clinical epigenetics, 15(1), 107. https://doi.org/10.1186/s13148-023-01524-7</p> <p>Background<br>In utero exposure to maternal hyperglycemia has been associated with an increased risk for the development of chronic diseases in later life. These predispositions may be programmed by fetal DNA methylation (DNAm) changes that persist postnatally. However, although some studies have associated fetal exposure to gestational hyperglycemia with DNAm variations at birth, and metabolic phenotypes in childhood, no study has yet examined how maternal hyperglycemia during pregnancy may be associated with offspring DNAm from birth to five years of age.</p> <p>Hypothesis<br>Maternal hyperglycemia is associated with variation in offspring DNAm from birth to 5 years of age.</p> <p>Methods<br>We estimated maternal hyperglycemia using the area under the curve for glucose (AUCglu) following an oral glucose tolerance test conducted at 24–30 weeks of pregnancy. We quantified DNAm levels in cord blood (n = 440) and peripheral blood at five years of age (n = 293) using the Infinium MethylationEPIC BeadChip (Illumina). Our total sample included 539 unique dyads (mother–child) with 194 dyads having DNAm at both time-points. We first regressed DNAm M-values against the cell types and child age for each time-point separately to account for the difference by time of measurement for these variables. We then used a random intercept model from the linear mixed model (LMM) framework to assess the longitudinal association between maternal AUCglu and the repeated measures of residuals of DNAm. We adjusted for the following covariates as fixed effects in the random intercept model: maternal age, gravidity, smoking status, child sex, maternal body mass index (BMI) (measured at first trimester of pregnancy), and a binary variable for time-point.</p> <p>Results<br>In utero exposure to higher maternal AUCglu was associated with lower offspring blood DNAm levels at cg00967989 located in FSD1L gene (β = − 0.0267, P = 2.13 × 10–8) in adjusted linear regression mixed models. Our study also reports other CpG sites for which DNAm levels were suggestively associated (P < 1.0 × 10–5) with in utero exposure to gestational hyperglycemia. Two of these (cg12140144 and cg07946633) were found in the promotor region of PRDM16 gene (β: − 0.0251, P = 4.37 × 10–07 and β: − 0.0206, P = 2.24 × 10–06, respectively).</p> <p>Conclusion<br>Maternal hyperglycemia is associated with offspring DNAm longitudinally assessed from birth to 5 years of age.</p> <p> </p> <p> </p>
Data from: Impact on offspring methylation patterns of maternal gestational diabetes mellitus and intrauterine growth restraint suggest common genes and pathways linked to subsequent type 2 diabetes risk
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Data from: Adaptive developmental plasticity in rhesus macaques: the serotonin transporter gene interacts with maternal care to affect juvenile social behaviour
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Data from: Maternal stress has divergent effects on gene expression patterns in the brains of male and female threespine stickleback
Maternal stress can have long-term effects on neurodevelopment that can influence offspring performance and population evolutionary trajectories. To examine the mechanistic basis for these neurodevelopmental effects of maternal stress, we used RNA-seq to assess differential gene expression across the brain transcriptome of adult male and female threespine stickleback (Gasterosteus aculeatus) from stressed and unstressed mothers. We identified sexually divergent effects of maternal stress on the brain transcriptome. In males, genes that were up-regulated by maternal stress were enriched for processes involved in synaptic function and organization and steroid hormone mediated signaling pathways, whereas in females genes that were up-regulated by maternal stress were enriched for processes involved in protein translation and metabolic functions. The expression of several genes involved in the hypothalamic-pituitary-interrenal response to stress and epigenetic processes such as the regulation of DNA methylation patterns and miRNAs increased in males and not in females. These data suggest that maternal stress has markedly different effects on cellular pathways in the brains of male and female offspring of mothers that are exposed to stress, which could have important implications when assessing the long-term ecological and evolutionary impacts of stress across generations.
The prenatal hypoxic pathology associated with maternal stress predisposes to dysregulated expression of the chrna7 gene and the subsequent development of nicotine addiction in adult offspring (Supplementary)
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Gene-Environment interactions in the influence of maternal education on adolescent neurodevelopment using ABCD Study
<p>Summary statistics for gene by maternal education effects</p>
Data from: Multi-year genetic sampling indicates maternal gene flow via colony emigrations in the army ant Eciton burchellii parvispinum
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Data from: Dynamic interpretation of maternal inputs by the Drosophila segmentation gene network
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Data from: Maternal stress has divergent effects on gene expression patterns in the brains of male and female threespine stickleback
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Impact of Maternal Immune Activation and Sex on Placental and Fetal Brain Cytokine and Gene Expression Profiles in a Preclinical Model of Neurodevelopmental Disorders
GEO Series GSE248222. Mus musculus. 64 samples. Type: Expression profiling by high throughput sequencing.
Nanog, SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal-to-zygotic transition
GEO Series GSE47558. Danio rerio. 35 samples. Type: Expression profiling by high throughput sequencing; Other.
Maternal Stress Triggers Early-Life Eczema via Fetal Mast Cell Reprogramming [10x Genomics Multiome ATAC + Gene Expression]
GEO Series GSE290848. Mus musculus. 8 samples. Type: Other.
Differential Gene Expression in Cdh13 KO x Maternally separated mice
GEO Series GSE119082. Mus musculus. 69 samples. Type: Expression profiling by high throughput sequencing.
Maternal age affects D8 embryo gene expression both in trophoblast and inner cell
GEO Series GSE162893. Equus caballus. 22 samples. Type: Expression profiling by high throughput sequencing.
Maternal Folate Genes and Aberrant DNA Hypermethylation among Offspring with Pediatric Lymphoblastic Leukemia
GEO Series GSE99793. Homo sapiens. 57 samples. Type: Methylation profiling by high throughput sequencing.
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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.