Oocyte methylation landscape
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Project description:ATAC sequencing of bovine oocytes and early embryos revealed a genome-wide map of accessible chromatin of bovine early embryo development, highlighting the critical features of chromatin landscape and epigenetic reprogramming during bovine preimplantation embryo development.
2020-11-21 | GSE145040 | GEO
Project description:Our data provided a genome-wide DNA methylation landscape of human early development embryos, including human MII oocytes, sperm, zygotes, 2-cell to 8-cell embryos, morula, blastocyst and postimplantation embryos at single base resolution. In total, 44 samples including biological and technical replicates, from 12 different human embryo development stages were analyzed, including two metaphase II oocytes, two zygotes, three first polar bodies, two second polar bodies, four sperm samples, two 2-cell-stage embryos, two 4-cell-stage embryos, three 8-cell-stage embryos, three morulae, three inner cell masses (ICMs) and three trophectoderms (TEs) seperated from late blastocysts, and three post-implantation embryos. In addition, 12 different human embryo development stages were analyzed, including metaphase II oocytes, zygotes, first polar bodies, second polar bodies, sperm samples, 2-cell-stage embryos, 4-cell-stage embryos, 8-cell-stage embryos, morulae, inner cell masses (ICMs) and trophectoderms (TEs) seperated from late blastocysts, and post-implantation embryos.
2014-07-22 | E-GEOD-49828 | biostudies-arrayexpress
Project description:We report the first genome-wide landscape of H3K9me2 ChIP-seq profile in mouse oocytes. We also performed whole-genome bisulfite sequencing and RNA-seq analysis of G9a conditional KO oocytes and maternal KO preimplantation embryos. Our findings illuminate the functional importance of G9a in preimplantation development and, in addition, pose a question on the proposed role for H3K9me2 in protection of the maternal genome from active CG demethylation.
2019-04-02 | GSE112320 | GEO
Project description:Our data provided a genome-wide DNA methylation landscape of human early development embryos, including human MII oocytes, sperm, zygotes, 2-cell to 8-cell embryos, morula, blastocyst and postimplantation embryos at single base resolution.
2014-07-22 | GSE49828 | GEO
Project description:10% of methylation sites in CpG islands. In this study, the genome-wide CpG islands of human sperm, oocyte and pre-implantation embryos were analyzed using the almost complete coverage of promoters and CpG islands (most methylation-producing regions) methylation microarray method (MeDIP-Chip). Dynamic changes in methylation of sub-regions to understand the dynamic pattern of CpG island and promoter methylation, possible regulatory mechanisms of this methylation dynamic change, and function during early embryonic development.
2020-02-01 | GSE124358 | GEO
Project description:We have performed deep RNA-Seq and de novo transcriptome assembly at different stages of mouse oogenesis. This revealed thousands of novel non-annotated genes as well as alternative promoters for ~10% of reference genes expressed in oocytes, a large fraction of which coincide with transposable elements of the MaLR and ERVK families. We defined the oocyte DNA methylation landscape as composed of large-scale hyper- and hypo-methylated domains. Correlation with our transcriptome assembly revealed that transcription correlates accurately with DNA methylation and potentially account for ~85-90% of the DNA methylome. RNA-Seq in mouse oocytes at different stages of folliculogenesis
2015-09-02 | E-GEOD-70116 | biostudies-arrayexpress
Project description:High resolution polysome fractionation and low-input ribosome profiling of bovine oocytes and preimplantation embryos has enabled us to define the translational landscape of early embryo development at an unprecedented level. We systematically and comparatively analyzed the transcriptome, polysome- and nonpolysome-bound RNA profiles of bovine oocytes and early embryos at 2-, 8-cell, morula, and blastocyst stage, and defined four modes of translational selectivity in bovine preimplantation embryo development: i. selective translation of non-abundant mRNAs, ii. active translating highly expressed mRNAs, iii. Translationally suppressed abundant mRNAs, and iv. Monosomaly occupied mRNAs. A strong selection towards genes involved in mitochondrial function and metabolic pathways was found throughout bovine preimplantation development. We found translatome largely follows transcriptome at oocytes, followed by a marked translational control at 8-cell embryos, which is gradually synchronized at the morula and blastocyst stage. We identified important novel cellular/embryonic functional regulators that being utilized and prioritized for translation at each developmental stage, that accompanies little-known bovine embryonic developmental programming. Together, these data reveal a unique spatiotemporal translational regulation that accompanies bovine preimplantation development.
2022-10-01 | GSE196484 | GEO
Project description:DNA methylation is an important epigenetic modification that undergoes dynamic changes in mammalian embryogenesis, during which both parental genomes are reprogrammed. Despite the many immunostaining studies that have assessed global methylation, the gene-specific DNA methylation patterns in bovine preimplantation embryos are unknown. Using reduced representation bisulfite sequencing, we determined genome-scale DNA methylation patterns of bovine sperm and individual in vivo developed oocytes and preimplantation embryos. We show that: 1) the major wave of genome-wide demethylation was completed by the 8-cell stage; 2) promoter methylation was significantly and inversely correlated with gene expression at the 8-cell and blastocyst stages; 3) sperm and oocytes have numerous differentially methylated regions (DMRs) - DMRs specific for sperm were strongly enriched in long terminal repeats (LTRs) and rapidly lost methylation in embryos, while the oocyte-specific DMRs were more frequently localized in exons and CpG islands (CGIs) and demethylated gradually across cleavage stages; 4) a unique set of DMRs were found between in vivo and in vitro matured oocytes; and 5) differential methylation between bovine gametes was confirmed in some but not all known imprinted genes. Our data provide insights into deciphering the complex epigenetic reprogramming of bovine early embryos and will serve as an important model for investigating human development and the evolutionary and regulatory roles of DNA methylation.
2018-08-01 | GSE110400 | GEO
Project description:Preimplantation embryo development is a precisely regulated process organized by maternally inherited and newly synthesized proteins. Recently, some studies have reported that blastocyst-like structures, named blastoids, can be generated from mouse ESCs (embryonic stem cells) or EPSCs (extended pluripotent stem cells). In this study, to explore the dynamic expression characteristics of proteins and their PTMs in mouse EPS blastoids, we revealed the protein expression profile of EPS-blastoids and metabolite characteristics by TMT-based quantitative mass spectrometry (MS) strategy. Furthermore, the protein phosphorylation sites were identified to show the phosphoproteomic analysis in blastoids compared with mouse early embryos. Above all, our study revealed the protein expression profile of EPS blastoids compared with mouse embryos during preimplantation development and indicated that glucose metabolism is key to blastoid formation.
2022-04-04 | PXD031002 | Pride