Histone chaperone CAF-1 is essential for retrotransposon silencing by mediating histone H4K20me3 deposition in mouse preimplantation embryos
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Kimiko Inoue
PROVIDER: E-GEOD-69260 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
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.
2015-11-01 | GSE69260 | GEO
Project description:The transition between morula and blastocyst stage during preimplantation development represents the first differentiation event of embryogenesis. Morula cells undergo the first cellular specialization and produce two well-defined populations of cells, the trophoblast and the inner cell mass (ICM). Embryonic stem cells (ESCs) with unlimited self-renewal capacity are believed to represent the in vitro counterpart of the ICM. Both mouse and rat ESCs can be derived from the ICM cells, but their in vitro stability differs. In this study we performed a microarray analysis in which we compared the transcriptome of mouse and rat morula, blastocyst, and ICM. This cross-species comparison represents a good model for understanding the differences in derivation and cultivation of ESCs observed in the two species. In order to identify alternative regulation of important molecular mechanisms the investigation of differential gene expression between the two species was extended at the level of signaling pathways, gene families, and single selected genes of interest. Some of the genes differentially expressed between the two species are already known to be important factors in the maintenance of pluripotency in ESCs, like for example Sox2 or Stat3, or play a role in reprogramming somatic cells to pluripotency like c-Myc, Klf4 and p53 and therefore represent interesting candidates to further analyze in vitro in the rat ESCs. This is the first study investigating the gene expression changes during the transition from morula to blastocyst in the rat preimplantation development. Our data show that in the pluripotent pool of cells of the rat and mouse preimplantation embryo substantial differential regulation of genes is present, which might explain the difficulties observed for the derivation and culture of rat ESCs using mouse conditions Casanova EA, Okoniewski MJ, Cinelli P. Cross-Species Genome Wide Expression Analysis during Pluripotent Cell Determination in Mouse and Rat Preimplantation Embryos.PLoS One. 2012;7(10):e47107. doi: 10.1371/journal.pone.0047107. Epub 2012 Oct 15. We collected morula and blastocysts stage embryos from mouse and rat and, by immunosurgery, we isolated the ICM cells from the blastocysts. All the embryos and ICMs were pooled into two groups for every developmental stage. Pooling of embryos for RNA extraction in this study was chosen mainly because of the low amounts of RNA that can be isolated from preimplantation embryos, and in addition because of the heterogeneity of the cell populations present in the embryos. For the analysis we pooled a large number (n >100) of the independent isolated embryos to achieve a sufficient accuracy of biological pooling . Due to the difficulties to isolate a larger number of embryos from mice and rats, we performed the microarray study by using two replicate samples per developmental stage.
2012-11-07 | E-GEOD-42081 | biostudies-arrayexpress
Project description:Histone chaperone CAF-1 is essential for retrotransposon silencing by mediating histone H4K20me3 deposition in mouse preimplantation embryos
| PRJNA285041 | ENA
Project description:Mammalian preimplantation development is a complex process involving dramatic changes in the transcriptional architecture. Through single-cell RNA-sequencing (RNA-seq), we report here a comprehensive analysis of transcriptome dynamics from oocyte to morula in both human and mouse embryos. Based on single nucleotide variants (SNVs) in blastomere mRNAs and paternal-specific SNPs, we identify novel stage-specific monoallelic expression patterns for a significant portion of polymorphic gene transcripts (25-53%). By weighted gene co-expression network analysis (WGCNA), we find that each developmental stage can be concisely delineated by a small number of functional modules of co-expressed genes. This result indicates a sequential order of transcriptional changes in pathways of cell cycle, gene regulation, translation, and metabolism in a step-wise fashion from cleavage to morula. Cross-species comparisons reveal that the majority of human stage-specific modules (7 out of 9) are remarkably preserved, only to diverge in developmental specificity and timing in mice. We further identify conserved key members (or hub genes) of the human and mouse networks. These genes represent novel candidates that are likely key players in driving mammalian preimplantation development. Collectively, we demonstrate that mammalian preimplantation development is orchestrated by evolutionarily conserved genetic programs that diverge in developmental timing. Our results provide a valuable resource to dissect gene regulatory mechanism underlying progressive development of early mammalian embryos. single-cell RNA-seq of human and mouse blastomeres
2013-07-29 | E-GEOD-44183 | biostudies-arrayexpress
Project description:Transcriptional profiling of mouse embryos spanning the 8-cell morula stage to E5.5 postimplantation epiblast was performed using lineage-specific RNA-seq.
2015-11-09 | E-MTAB-2958 | biostudies-arrayexpress
Project description:Endocannabinoid signaling plays a key role in multiple events in female reproduction. In this investigation, we discovered an interesting phenomenon that mice with either elevated or silenced endocannabinoid signaling show similar defects in multiple pregnancy events, including preimplantation embryo development. To unravel the underlying mechanisms, microarray studies were was conducted using RNAs collected from WT, Cnr1-/- and Faah-/- mouse blastocysts on day 4 of pregnancy. The results show that about 100 genes showed unidirectional changes under either elevated or silenced endocannabinoid signaling. Analysis of functional grouping of these genes revealed that multiple biological functions and pathways are affected under aberrant endocannabinoid signaling, including cell migration. Several genes from the microarray data were confirmed by quantitative RT-PCR. Cell motility assays validated the predicted compromised cell migration in Cnr1-/- and Faah-/- trophoblast stem cells. This study provides molecular basis for biphasic effects of endocannabinoid signaling in female reproduction To generate Cnr1-/-, Faah-/- and WT embryos, mutant and WT females were mated with males of the same genotypes. On day 4 of pregnancy at 1500h, embryos were collected from oviducts and uteri of pregnant females, because Cnr1-/- and Faah-/- females show aberrant oviductal transport of embryos. As expected, WT embryos were mostly at the blastocyst stage and all of them were collected from uteri. However, Cnr1-/- and Faah-/- females had higher percentages of embryos at the morula stage, and some of them were still in the oviduct. Since gene expression profiles greatly vary depending on the embryonic development stage, morulae were not included in gene expression analysis; only RNAs from blastocysts were used to better understand the effects solely arising from disrupted cannabinoid signaling in blastocysts.
2012-07-25 | E-GEOD-36399 | biostudies-arrayexpress
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.
2023-03-11 | PXD035294 | Pride
Project description:Early embryo development is a dynamic process involving important molecular and structural changes leading to the embryonic genome activation (EGA) and first cell lineage differentiation. Our aim was to elucidate proteomic changes in bovine embryos developed in vivo. Eleven Holstein females were used as embryo donors and pools of embryos at the 4-6 cell, 8-12 cell, morula, compact morula and blastocyst stages were analyzed by nanoliquid chromatography coupled with tandem MS (nanoLC-MS/MS). A total of 2757 proteins were identified, of which 1950 were quantitatively analyzed. Principal component analysis of data showed a separation of embryo pools according to their developmental stage. Differentially abundant proteins (DAPs) between stages were clustered into 626 upregulated and 400 downregulated proteins with most significant changes at the time of EGA and blastocyst formation. The main pathways and processes overrepresented among upregulated proteins were RNA metabolism, protein translation and ribosome biogenesis whereas Golgi vesicle transport and protein processing in endoplasmic reticulum were overrepresented among downregulated proteins. This is the first comprehensive study of proteome dynamics in non-rodent mammalian embryos developed in vivo. These data provide a number of functional protein candidates and will be useful to evaluate the impact of in vitro conditions on embryo quality.
2022-05-20 | PXD030994 | Pride
Project description:Post-translational modifications (PTMs) of histones exert fundamental roles in regulating gene expression. During development, groups of PTMs are constrained by unknown mechanisms into combinatorial patterns, which facilitate transitions from uncommitted embryonic cells into differentiated somatic cell lineages. Repressive histone modifications such as H3K9me3 or H3K27me3 have been investigated in detail, but the role of H4K20me3 in development is currently unknown. Here we show that Xenopus laevis Suv4-20h1 and h2 histone methyltransferases (HMTases) are essential for induction and differentiation of the neuroectoderm. Morpholino-mediated knockdown of the two HMTases leads to a selective and specific downregulation of genes controlling neural induction, thereby effectively blocking differentiation of the neuroectoderm. Global transcriptome analysis supports the notion that these effects arise from the transcriptional deregulation of specific genes rather than widespread, pleiotropic effects. Interestingly, morphant embryos fail to repress the Oct4-related Xenopus gene Oct-25. We validate Oct-25 as direct target of xSu4-20h enzyme-mediated gene repression, showing by chromatin immunoprecipitaton that it is decorated with the H4K20me3 mark downstream of the promoter in normal, but not in double-morphant, embryos. Since knockdown of Oct-25 protein significantly rescues the neural differentiation defect in xSuv4-20h double-morphant embryos, we conclude that the epistatic relationship between Suv4- 20h enzymes and Oct-25 controls the transit from pluripotent to differentiation-competent neural cells. Consistent with these results in Xenopus, murine Suv4-20h1/h2 double-knockout embryonic stem (DKO ES) cells exhibit increased Oct4 protein levels before and during EB formation, and reveal a compromised and biased capacity for in vitro differentiation, when compared to normal ES cells. Together, these results suggest a regulatory mechanism, conserved between amphibian and mammals, in which H4K20me3-dependent restriction of specific POU-V genes directs cell fate decisions, when embryonic cells exit the pluripotent state. Total RNA samples from Xenopus laevis embryos. Transcript levels were analyzed after injection of control or Suv420 morpholinos into blastomeres.
2013-02-06 | E-GEOD-41256 | biostudies-arrayexpress
Project description:Cloning mammals by somatic cell nuclear transfer (SCNT) is highly inefficient. Most SCNT-generated embryos die after implantation because of unidentified, complex epigenetic errors in the process of postimplantation embryonic development. Here, we identified the most upstream level of dysfunction leading to impaired development of clones by using RNA interference (RNAi) against Xist, a gene responsible for X chromosome inactivation (XCI). A prior injection of Xist-specific short interfering (si)RNA into reconstructed oocytes efficiently corrected the SCNT-specific aberrant Xist expression at the morula stage, but failed to do so thereafter at the blastocyst stage. However, we found that shortly after implantation this aberrant XCI status in cloned embryos had been corrected autonomously in both embryonic and extraembryonic tissues, probably through a newly established XCI control for postimplantation embryos. Embryo transfer experiments revealed that the siRNA-treated embryos showed 10 times higher survival than controls as early as embryonic day 5.5 and this high survival persisted until term, resulting in a remarkable improvement in cloning efficiency (12% vs. 1% in controls). Importantly, unlike control clones, these Xist-siRNA clones at birth showed only a limited dysregulation of their gene expression, indicating that correction of Xist expression in preimplantation embryos had a long-term effect on their postnatal normality. Thus, contrary to the general assumption, our results suggest that the fate of cloned embryos is determined almost exclusively before implantation by their XCI status. Furthermore, our strategy provides a promising breakthrough for mammalian SCNT cloning because RNAi treatment of oocytes is readily applicable to most mammal species. Gene expression were measured in mouse in vitro fertilized and somatic cell cloned embryos. Four biological replicates were performed in each group of Xist- or Control-siRNA.
2011-11-17 | E-GEOD-33208 | biostudies-arrayexpress