ChIP-seq profile in in vitro produced mouse morula stage embryos treated with siRNA targeting Pcgf5
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ABSTRACT:
PROVIDER: PRJNA1181527 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31204754_1.fastq.gz | Fastqsanger.gz | |||
| SRR31204754_2.fastq.gz | Fastqsanger.gz | |||
| SRR31204755_1.fastq.gz | Fastqsanger.gz | |||
| SRR31204755_2.fastq.gz | Fastqsanger.gz | |||
| SRR31204756_1.fastq.gz | Fastqsanger.gz |
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Project description:We obtained H3K27me3 profiles in mouse morula stage embryos (72 h post-insemination (hpi)) which had been in vitro treated with siRNA targeting Pcgf5 from one-cell stage (3 hpi).
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Project description:Background: The transcriptional changes around the time of embryonic genome activation in pre-implantation embryos indicate that this process is highly dynamic. In vitro produced porcine blastocysts are known to be less competent than in vivo developed blastocysts. To understand the conditions that compromise developmental competence of in vitro embryos, it is crucial to evaluate the transcriptional profile of porcine embryos during pre-implantation stages. In this study, we investigated the transcriptome dynamics in in vivo developed and in vitro produced 4-cell embryos, morulae and hatched blastocysts. Results: In vivo developed and in vitro produced embryos displayed largely similar transcriptome profiles during development. Enriched canonical pathways from the 4-cell to the morula transition that were shared between in vivo developed and in vitro produced embryos included oxidative phosphorylation and EIF2 signaling. The shared canonical pathways from the morula to the hatched blastocyst transition were 14-3-3-mediated signaling, xenobiotic metabolism general signaling pathway, and NRF2-mediated oxidative stress response. The in vivo developed and in vitro produced hatched blastocysts were compared to identify molecular signaling pathways indicative of lower developmental competence of in vitro produced hatched blastocysts. A higher metabolic rate and expression of the arginine transporter SLC7A1 were found in in vitro produced hatched blastocysts. Conclusions: Our findings suggest that embryos with compromised developmental potential are arrested at an early stage of development, while embryos developing to the hatched blastocyst stage display largely similar transcriptome profiles, irrespective of the embryo source. The hatched blastocysts derived from the in vitro fertilization-pipeline showed an enrichment in molecular signaling pathways associated with lower developmental competence, compared to the in vivo developed embryos.
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Project description:We obtained genome-wide profiles of histone H3 lysine 27 trimethylation (H3K27me3) in bovine morula which had been in vitro treated with a methionine adenosyltransferase 2A (MAT2A) inhibitor from the 8-16 cell stage. Sequencing center: NODAI Genome Research Center, Tokyo University of Agriculture
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Project description:YY1 plays multifaceted roles in various cell types. We recently reported that YY1 regulates nucleosome organization in early mouse embryos (Sakamoto et al. Genes Dev 2023). However, despite the impaired nucleosome organization in the absence of YY1, the transcriptome was minimally affected in eight-cell embryos. We then hypothesized that YY1 might prepare a chromatin environment to regulate gene expression at later stages. To test this possibility, we performed a transcriptome analysis at the morula stage. We found that a substantial number of genes are aberrantly expressed in the absence of YY1. Furthermore, our analysis revealed that YY1 is required for the transcription of retrotransposons in early embryos.
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Project description:Early bovine cleavage (day 0 to 3) was treated with high glucose (5mM) or control glucose (0.2mM) then total day 3 embryos were cultured in control condition until day 5 when gene expression was assessed in developping morula by microarray
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Project description:We perform single-cell profiling of chromatin accessibility, DNA methylation, and transcription (scNMT-seq) in marmoset embryos at the four-cell, eight-cell, and compacted morula stages. This dataset corresponds to the transcriptome component.
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Project description:Despite many improvements with in vitro culture systems, the quality and developmental ability of mammalian embryos produced in vitro is still lower than their in vivo counterparts. To bring knowledge to answer this question, we used a mass spectrometry (MS) approach to compare the protein content of bovine embryos that were conceived in vivo or produced in vitro. A total of 38 pools of grade-1 quality bovine embryos at the 4-6 cell, 8-12 cell, morula, compact morula and blastocyst stages developed either in vivo or in vitro were analyzed by nano-liquid chromatography coupled with label-free quantitative mass spectrometry, allowing the identification of 3,028 proteins. Multivariate analysis of quantified proteins showed a clear separation of embryo pools according to their in vivo or in vitro origin at all stages. Three clusters of differentially abundant proteins (DAPs) according to embryo origin were evidenced, including 463 proteins more abundant in vivo than in vitro across development, and 314 and 222 proteins more abundant in vitro than in vivo before and after the morula stage, respectively. The functional analysis of proteins found more abundant in vivo showed an enrichment in carbohydrate metabolism and cytoplasmic cellular components. Proteins found more abundant in vitro before the morula stage were mostly localized in mitochondrial matrix and involved in ATP-dependent activity while those overabundant after morula stage were mostly localized in the ribonucleoprotein complex and involved in protein synthesis. Oviductin and other proteins previously shown to interact with early embryos in vitro were among the most overabundant proteins after in vivo development. In conclusion, the maternal environment led to faster degradation of mitochondrial proteins at early embryo developmental stages, lower abundance of proteins involved in protein synthesis at the time of embryonic genome activation and a global upregulation of carbohydrate and small molecule metabolic pathways compared to in vitro produced embryos. Furthermore, our data confirm that embryos developed in vivo uptake large amounts of oviduct fluid-derived proteins as soon as the 4-6 cell stage. These data provide new insight into the molecular contribution of the mother to the developmental ability of early embryos and will help designing better in vitro culture systems.
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Project description:Retrotransposons are widely spread in the mammalian genome and are usually silenced during development to avoid transposition-inducing mutations. But how they are repressed in embryos shortly before implantation remain to be identified, since the genome at this stage is globally hypomethylated. Here we show a histone chaperon, CAF-1, is responsible for retrotransposon silencing at the morula-blastocyst stages by depositing histone H4 lysine 20 trimethylation (H4K20me3). Knockdown of CAF-1 with a specific siRNA resulted in derepression of LINE-1, SINE-B2 and IAP associated with the decreased H4K20me3 level, and arrested embryonic development at the morula stage. The identical results were obtained with siRNAs against Suv420h1/2, H4K20 methyltransferases. Treatment with reverse transcriptase inhibitors rescued at least a part of these embryos. Thus, CAF-1 ensures the genomic integrity of preimplantation embryos by establishing repressive histone marks in the multiple retrotransposon classes. Comparative gene expression analyses using P150 knockdown (P150KD) embryos at morula stage were performed by microarray. P150KD embryos were produced with the injection of P150 siRNA into 1-cell embryos. As controls, siControl embryos were produced by the injection of control siRNA. These embryos were subjected to gene expression microarray.
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Project description:Pre-implantation embryos derived by in vitro fertilization differ in their developmental potential from embryos obtained in vivo. In order to characterize changes in gene expression profiles caused by in vitro culture environment, we employed microarray constructed from bovine embryo-specific cDNAs (BlueChip v., Université Laval, Québec) to compare in vitro cultured and in vivo derived bovine embryos at 4-cell and 8-cell stage.
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Project description:This study aimed to compare the transcriptome of vitrified and slow frozen embryos with the untreated control. Bovine embryos (compact morulae) were vitrified or slow frozen and post-warm embryos were cultured to expanded blastocyst stage. The vitrified- and slow frozen-derived were subjected to microarray analysis and compared with untreated control embryos for differential gene expression. Morula to blastocyst conversion rate was higher (P<0.05) in control (72%) and vitrified (77%) embryos compared to slow frozen (34%) embryos. Total 20 genes were upregulated and 44 genes were downregulated in the vitrified embryos (fold change ≥ +-2, P<0.05). In slow frozen embryos, 102 genes were upregulated and 63 genes were downregulated (fold change ≥ +-1.5, P<0.05) in comparison with untreated embryos. Vitrified embryos exhibited significant changes in gene expression mainly involving embryo implantation (PTGS2, CALB1), lipid peroxidation and ROS generation (HSD3B1, AKR1B1, APOA1) and cell differentiation (KRT19, CLDN23). The slow frozen embryos, however, showed significant changes in the expression of genes related to cell signaling (SPP1), cell structure and differentiation (DCLK2, JAM2 and VIM), and lipid metabolism (PLA2R1 and SMPD3). In silico comparison between vitrified and slow-frozen (reference) embryos revealed similar changes in gene expression as between vitrified and untreated embryos. In conclusion, the vitrified bovine embryos demonstrated better post-warming embryo development than slow-frozen bovine embryos but their gene expression related to lipid metabolism, steroidogenesis, cell differentiation and placentation changed significantly. Slow freezing killed more embryos than vitrification, and the survived embryos did not express significant change in their gene expression.
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