Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1006508 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In this study, we performed ChIP-seq of RNA polymerase II, phosphorylated RNA polymerase II and related epigenetic modifications to elucidate transcriptional activities of mouse oocytes and preimplantation embryos. Through analyzing epigenetic alterations of transgenically-modified growing oocytes, early embryos from aged female, and early embryos treated with drugs disturbing proteostasis, we identified critical roles of proteostasis in transcriptional regulation of mouse oocytes and early embryos.
2025-01-20 | GSE241246 | GEO
Project description:In this study, we performed RNA-seq to elucidate how transcriptional activities of mouse oocytes and preimplantation embryos are regulated to control oocyte-to-embryo transition. Through analyzing transcriptome alterations of transgenically-modified growing oocytes, early embryos from aged female, early embryos treated with drugs disturbing proteostasis, and embryonic stem cells treated with drugs disturbing proteostasis, we identified critical roles of proteostasis in transcriptional regulation of mouse oocytes and early embryos.
2025-01-20 | GSE241388 | GEO
Project description:MicroRNA function is globally suppressed in mouse oocytes and early embryos
| PRJNA122039 | ENA
Project description:Sex differences in liver gene expression are dictated by sex-differences in circulating growth hormone (GH) profiles. Presently, the pituitary hormone dependence of mouse liver gene expression was investigated on a global scale to discover sex-specific early GH response genes that might contribute to sex-specific regulation of downstream GH targets and to ascertain whether intrinsic sex-differences characterize hepatic responses to plasma GH stimulation. RNA expression analysis using 41,000-feature microarrays revealed two distinct classes of sex-specific mouse liver genes: genes subject to positive regulation (class-I) and genes subject to negative regulation by pituitary hormones (class-II). Genes activated or repressed in hypophysectomized (Hypox) mouse liver within 30-90min of GH pulse treatment at a physiological dose were identified as direct targets of GH action (early response genes). Intrinsic sex-differences in the GH responsiveness of a subset of these early response genes were observed. Notably, 45 male-specific genes, including five encoding transcriptional regulators that may mediate downstream sex-specific transcriptional responses, were rapidly induced by GH (within 30min) in Hypox male but not Hypox female mouse liver. The early GH response genes were enriched in 29 male-specific targets of the transcription factor Mef2, whose activation in hepatic stellate cells is associated with liver fibrosis leading to hepatocellular carcinoma, a male-predominant disease. Thus, the rapid activation by GH pulses of certain sex-specific genes is modulated by intrinsic sex-specific factors, which may be associated with prior hormone exposure (epigenetic mechanisms) or genetic factors that are pituitary-independent, and could contribute to sex-differences in predisposition to liver cancer or other hepatic pathophysiologies.
2010-01-27 | GSE17644 | GEO
Project description:Transcriptome analysis of oocytes and early embryos to demonstrate trancriptional regulation during mouse oocyte-to-embryo transition
| PRJNA1006851 | ENA
Project description:DNA methylation is a tightly regulated epigenetic mark associated with transcriptional repression. Next-generation sequencing of purified methylated DNA obtained from early Xenopus tropicalis embryos demonstrates that this genome is heavily methylated during blastula and gastrula stages. Although DNA methylation is largely absent from transcriptional start sites marked with histone H3 lysine 4 trimethylation (H3K4me3), we find both promoters and gene bodies of active genes robustly methylated. By contrast, DNA methylation is absent in large H3K27me3 domains, indicating these two repression pathways have different roles. Comparison with chromatin state maps of human ES cells reveals strong conservation of epigenetic makeup and gene regulation between the two systems. Strikingly, genes that are highly expressed in human pluripotent cells and in Xenopus embryos but not in differentiated cells exhibit relatively high methylation in both promoters and gene bodies in embryos. Therefore we tested the repressive potential of DNA methylation using transient and transgenic approaches and show that methylated promoters are robustly transcribed in blastula and gastrula-stage embryos, but not in oocytes or late embryos where methylated templates are repressed efficiently. These findings have implications for reprogramming and the epigenetic regulation of pluripotency and differentiation, suggesting a relatively open, pliable chromatin state in early embryos followed by re-established methylation-dependent transcriptional repression during organogenesis and differentiation. MethylCap (methylated DNA affinity capture with the MBD domain of MeCP2), 500mM and 700mM elution fractions of stage 9 (blastula) and stage 12.5 (gastrula) Xenopus tropicalis DNA
2011-06-23 | E-GEOD-23913 | biostudies-arrayexpress
Project description:Introgressed variants from other species can be an important source of genetic variation because they may arise rapidly, can include multiple mutations on a single haplotype, and have often been pretested by selection in the species of origin. Although introgressed alleles are generally deleterious, several studies have reported introgression as the source of adaptive alleles-including the rodenticide-resistant variant of Vkorc1 that introgressed from Mus spretus into European populations of Mus musculus domesticus. Here, we conducted bidirectional genome scans to characterize introgressed regions into one wild population of M. spretus from Spain and three wild populations of M. m. domesticus from France, Germany, and Iran. Despite the fact that these species show considerable intrinsic postzygotic reproductive isolation, introgression was observed in all individuals, including in the M. musculus reference genome (GRCm38). Mus spretus individuals had a greater proportion of introgression compared with M. m. domesticus, and within M. m. domesticus, the proportion of introgression decreased with geographic distance from the area of sympatry. Introgression was observed on all autosomes for both species, but not on the X-chromosome in M. m. domesticus, consistent with known X-linked hybrid sterility and inviability genes that have been mapped to the M. spretus X-chromosome. Tract lengths were generally short with a few outliers of up to 2.7 Mb. Interestingly, the longest introgressed tracts were in olfactory receptor regions, and introgressed tracts were significantly enriched for olfactory receptor genes in both species, suggesting that introgression may be a source of functional novelty even between species with high barriers to gene flow.
| S-EPMC8784167 | biostudies-literature
Project description:Current models of early development assign major roles to stochastic processes and epigenetic regulation, whose influence is considered to outweigh the genetic differences that exist between individuals. However, epigenetic agents are ultimately encoded by genes. It follows that the variable endowment of oocytes in these genes’ products could influence, prime or even predetermine developmental trajectories and features of embryos. As model system we used inbred strains of mice (129/Sv, C57Bl/6, C3H/HeN, DBA/2J). We examined if and in how far the composition of oocytes is conserved after we observed large variability in developmental competence and embryo quality across the four strains. Using state-of-the-art proteomics (SILAC LC-MS/MS) combined with transcriptomics (RNA deep sequencing) we quantified 2012 protein groups and 15205 transcripts present simultaneously in oocytes of all four strains. Proteome and transcriptome expression levels had little correlation with each other, whereby the endowment of oocytes in proteins with known or putative function in embryo development could not be predicted from mRNA abundance. Our data show that depending on the oocyte donor strain, resultant embryos have different qualities that correlate with the abundance of catalytic proteins, highlighting the importance of proteomic quantifications in modern embryology. Thus, different strains of mice should not be used interchangeably when tackling questions about oogenesis and early development, and a variety of strains should be studied to yield results of sufficient general validity.
2015-01-28 | PXD001059 | Pride
Project description:Translational research is commonly performed in the C57B6/J mouse strain, chosen for its genetic homogeneity and phenotypic uniformity. Here, we evaluate the suitability of the white-footed deer mouse (Peromyscus leucopus) as a model organism for aging research, offering a comparative analysis against C57B6/J and diversity outbred (DO) Mus musculus strains. Our study includes comparisons of body composition, skeletal muscle function, and cardiovascular parameters, shedding light on potential applications and limitations of P. leucopus in aging studies. Notably, P. leucopus exhibits distinct body composition characteristics, emphasizing reduced muscle force exertion and a unique metabolism, particularly in fat mass. Cardiovascular assessments showed changes in arterial stiffness, challenging conventional assumptions and highlighting the need for a nuanced interpretation of aging-related phenotypes. Our study also highlights inherent challenges associated with maintaining and phenotyping P. leucopus cohorts. Behavioral considerations, including anxiety-induced responses during handling and phenotyping assessment, pose obstacles in acquiring meaningful data. Moreover, the unique anatomy of P. leucopus necessitates careful adaptation of protocols designed for Mus musculus. While showcasing potential benefits, further extensive analyses across broader age ranges and larger cohorts are necessary to establish the reliability of P. leucopus as a robust and translatable model for aging studies.
| S-EPMC11335981 | biostudies-literature