Rat oocyte epigenomes
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA769697 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16249241.fastq.gz | Fastqsanger.gz | |||
| SRR16249242.fastq.gz | Fastqsanger.gz | |||
| SRR16249243.fastq.gz | Fastqsanger.gz | |||
| SRR16249244.fastq.gz | Fastqsanger.gz | |||
| SRR16249245.fastq.gz | Fastqsanger.gz |
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Project description:The rat is a widely used model for human physiology and psychology. However, due to their longer gestation periods and husbandry costs relative to mice, as well as the availability of superior molecular techniques to manipulate the mouse genome, relatively few genome-wide studies have been conducted in the rat. As such, a comprehensive analysis of genomic imprinting, which impacts complex traits such as growth and behaviour, has yet to be conducted in the rat. Towards this end, we systematically profiled embryonic and extra-embryonic tissue gene expression and DNA methylation with allele-specific resolution. We identified 14 embryonic and 26 extra-embryonic imprinted genes in the rat. Comparative analyses with mouse revealed that orthologous imprinted gene expression and associated canonical DNA methylation imprints are conserved in the embryo proper of the Muridae family. However, only 3 paternally expressed imprinted genes in the extra-embryonic embryo are conserved in Muridae, all of which are associated with non-canonical H3K27me3 imprints. The discovery of 8 novel candidate non-canonical imprinted genes unique to the rat is consistent with more rapid evolution of extra-embryonic imprinting. Cross-species analysis of novel rat imprinted genes with mouse and human revealed multiple mechanisms by which species-specific imprinted expression may be established, including H3K27me3 deposition in the oocyte, the birth of ZFP57 binding motifs and the insertion of endogenous retroviral promoters. Thus, characterization of the rat imprintome provides insights into the conservation of imprinted gene expression and the etiology of species-specific imprinting.
2023-01-19 | GSE185573 | GEO
Project description:Gene expression profiles of granulosa cells from rat ovarian follicles by Affymetrix rat whole genome array showed that twelve genes were up-regulated, while one gene down-regulated more than 1.5 folds in the normal developmental competence group compared with those in the poor developmental competence group. Gene ontology classification showed that the up-regulated genes included lysyl oxidase and nerve growth factor receptor associated protein 1, which are important in the regulation of protein-lysine 6-oxidase activity, and in apoptosis induction, respectively. The down-regulated genes included glycoprotein-4-beta galactosyltransferase 2, which is involved in the regulation of extracellular matrix organization and biogenesis. Experiment Overall Design: Immature rats were injected with eCG and 24h thereafter with anti-eCG antibody to induce follicular atresia or with pre-immune serum to stimulate follicle development. A high percentage (30-50%, normal developmental competence, NDC) of oocytes from eCG/pre-immune serum group developed to term after embryo transfer compared to those from eCG/anti-eCG (0%, poor developmental competence, PDC). Gene expression profiles of granulosa cells from the above oocyte-collected follicles were assessed by Affymetrix rat whole genome array.
2008-06-15 | E-GEOD-7697 | biostudies-arrayexpress
Project description:The genetic causes of oocyte meiotic deficiency (OMD), a form of primary infertility characterised by the production of immature oocytes, remain largely unexplored. Using whole exome sequencing, we found that 26% of a cohort of 23 subjects with OMD harboured the same homozygous nonsense pathogenic mutation in PATL2, a gene encoding a putative RNA-binding protein. Using Patl2 knockout mice, we confirmed that PATL2 deficiency disturbs oocyte maturation, since oocytes and zygotes exhibit morphological and developmental defects respectively. PATL2's amphibian orthologue is involved in the regulation of oocyte mRNA as a partner of CPEB. However, Patl2's expression profile throughout oocyte development in mice, alongside colocalisation experiments with Cpeb1, Msy2 and Ddx6 (three oocyte RNA-regulators) suggest an original role for Patl2 in Mammals. Accordingly, transcriptomic analysis of oocytes from WT and Patl2-/- animals demonstrated that in the absence of Patl2, expression levels of a select number of highly relevant genes involved in oocyte maturation and early embryonic development are deregulated. In conclusion, PATL2 is a novel actor of mammalian oocyte maturation whose invalidation causes OMD in humans.
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Project description:Epigenomes of Hemin exposed trained monocytes
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Project description:Epigenomes of oxLDL exposed trained monocytes
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Project description:Study question: Are the molecular signatures of cumulus cells (CCs) and follicular fluid (FF) of adolescents undergoing fertility preservation differ from that of reproductively adult oocyte donors? Summary answer: The microenvironment immediately surrounding the oocyte, including the CCs and FF, is altered in adolescents undergoing fertility preservation compared to oocyte donors. What is known already: Adolescents experience a period of subfecundity following menarche. Recent evidence suggests that this may be at least partially due to increased oocyte aneuploidy. Reproductive juvenescence in mammals is associated with suboptimal oocyte quality. Study design, size, duration: This was a prospective cohort study. Adolescents (10-19 years old, N=23) and oocyte donors (22-30 years old, N=31) undergoing ovarian stimulation and oocyte retrieval at the Northwestern Fertility and Reproductive Medicine Center between November 1, 2020 and May 1, 2023 were enrolled in this study. Participants/materials, setting, method: Patient demographics, ovarian stimulation, and oocyte retrieval outcomes were collected for all participants. The transcriptome of CCs associated with mature oocytes was compared between adolescents (10-19 years old, n=19), and oocyte donors (22-30 years old, n=19) using bulk RNA-sequencing. FF cytokine profiles (10-19 years old, n=18 vs. 25-30 years old, n=16) were compared using cytokine arrays. Main results and the role of chance: RNA-seq analysis revealed 581 differentially expressed genes (DEGs) in cumulus cells of adolescents relative to oocyte donors, with 361 genes downregulated and 220 upregulated. Genes enriched in pathways involved in cell cycle and cell division (e.g., GO:1903047, p= 3.5 x 10-43; GO:0051983, p= 4.1 x 10- 30; GO:0000281, p= 7.7 x 10-15; GO:0044839, p= 5.3 x 10-13) were significantly downregulated, while genes enriched in several pathways involved in cellular and vesicle organization (e.g., GO:0010256, p= 1.2 x 10-8; GO:0051129, p= 6.8 x 10-7; GO:0016050, p= 7.4 x 10-7; GO:0051640, p= 8.1 x 10-7) were upregulated in CCs of adolescents compared to oocyte donors. The levels of 9 cytokines were significantly increased in FF of adolescents compared to oocyte donors: IL-1 alpha (2-fold), IL-1 beta (1.7-fold), I-309 (2-fold), IL-15 (1.6-fold), TARC (1.9-fold), TPO (2.1-fold), IGFBP-4 (2-fold), IL-12-p40 (1.7-fold) and ENA-78 (1.4-fold). Interestingly, 7 of these cytokines have known pro-inflammatory roles. Importantly, neither the CC transcriptomes or FF cytokine profiles were different in adolescents with or without cancer. Large scale data: Original high-throughput sequencing data will be deposited in Gene Expression Omnibus (GEO) before publication, and the GEO accession number will be provided here. Limitations, reasons for caution: This study aims to gain insights into the associated gamete quality by studying the immediate oocyte microenvironment. The direct study of oocytes is more challenging due to sample scarcity, as they are cryopreserved for future use, but will provide a more accurate assessment of oocyte reproductive potential. Wider implications of the findings: Understanding the underpinnings of altered immediate oocyte microenvironment of adolescent patients may provide insights into the reproductive potential of the associated gametes in the younger end of the age spectrum. This has implications for the fertility preservation cycles for very young patients.
2024-05-15 | GSE265995 | GEO
Project description:To find genes in C. elegans oocytes associated with reproductive aging. Five replicates comparing RNA from oocyte samples collected from day 3 fem-1(hc17) animals with RNA from oocyte samples collected from day 8 fem-1(hc17) animals. Three out of five are dye-flipped.
2010-09-01 | E-GEOD-23447 | biostudies-arrayexpress
Project description:The oocyte microenvironment is altered in adolescents compared to oocyte donors.
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Project description:During early mammalian development, DNA methylation undergoes two waves of reprogramming, enabling transitions between somatic cells, oocyte and embryo. The first wave of de novo DNA methylation establishment occurs in the oocytes. Its molecular mechanisms has been studied in mouse, a classical mammalian model. Current dogma describes DNA methyltransferase 3A (DNMT3A) and its cofactor DNMT3L as two essential factors for oocyte DNA methylation – the ablation of either leads to nearly complete abrogation of DNA methylation. However, DNMT3L is not expressed in human oocytes, suggesting that the mechanism uncovered in mouse is not universal across mammals. We analyzed available RNA-seq datasets from oocytes of multiple mammals including our novel naked mole-rat oocytes dataset, and revealed that Dnmt3l is expressed only in the oocytes of mouse, rat and golden hamster. We identified a specific promoter sequence recognised by an oocyte transcription factor complex associated with Dnmt3l activity and demonstrated that it emerged in the rodent clade Eumuroida, comprising the families Muridae (mice, rats, gerbils) and Cricetidae (hamsters). Therefore, Dnmt3l is expressed and consequently plays a role in de novo DNA methylation only in the oocytes of these species, instead of being an essential pan-mammalian factor.
2023-11-13 | GSE236457 | GEO
Project description:The objective of this study was to identify the expression profile of miRNAs in porcine oocytes derived from follicles of different sizes using RNA high throughput sequencing technology. Oocytes were aspirated from large (3-6 mm) or small (<2 mm) ovarian follicles and tested for developmental competence and chromatin configurations. Small RNA libraries were constructed from both groups and then sequenced on an Illumina NextSeq500. Oocytes from large follicles showed higher developmental competence and different chromatin configuration compared to small oocyte group. In total, 167 and 162 known miRNAs were detected in large and small oocyte groups, respectively with 153 miRNAs were commonly expressed in both groups. In addition, 155 predicted novel miRNAs were detected and quantified. MiR-205, miR-16, miR-148a-3p, miR-125b, and let-7 family were among the top 10 highly abundantly expressed miRNAs in both oocyte groups. Further analysis showed that 8 miRNAs were differentially expressed (DE) between both groups (>2 fold change) with 4 up- and 4 down-regulated miRNAs in large compared to small oocyte group. Target gene prediction followed by KEGG pathway analysis revealed 46 pathways that were enriched with miRNA-target genes. Oocyte meiosis pathway and signaling pathways including FoxO, PI3K-Akt, TGFβ, and cAMP were predictably targeted by DE miRNAs. These results give more insights into the potential role of miRNAs in controlling oocyte developmental competence.
2019-02-13 | GSE122032 | GEO