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Comprehensive analysis of H3K9me2 oocytes, together with DNA methylation and expression analysis of G9a conditional KO oocytes and maternal KO preimplantation embryos

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE112320 | GEO | 2019/04/02

REPOSITORIES: GEO

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Comprehensive analysis of H3K9me2 oocytes, together with DNA methylation and expression analysis of G9a conditional KO oocytes and maternal KO preimplantation embryos

Project description:Comprehensive analysis of H3K9me2 oocytes, together with DNA methylation and expression analysis of G9a conditional KO oocytes and maternal KO preimplantation embryos

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RNA-seq of oocytes and zygotes from pabpn1l ko and wt female mice

Project description:PABPN1L participates in the process of post-transcriptional regulation and degradation of maternal mRNA.We collect samples of each period from pabpn1l ko and wt female mice during different stages. Each group contained a total of 30 oocytes or zygotes. In the initial step, we spiked 2 × 106 mRNA-EGFP, transcribed in vitro, into each group.Then, RNA was extracted and detected.Reverse transcription was performed on the samples that met the effective concentration.After quality inspection, build the library.GV oocytes, MII oocytes and zygotes were collected from three different PABPN1L KO or WT mice seperately.

2021-03-26 | E-MTAB-10233 | biostudies-arrayexpress

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Project description:Early mouse development is accompanied by dynamic changes in chromatin modifications, including G9a-mediated histone H3 lysine 9 dimethylation (H3K9me2), which is essential for embryogenesis. Here we show that H3K9me2 directs repression of 2-cell stage specific genes in nascent embryos to facilitate preimplantation development. Thereafter, genome-wide accumulation of H3K9me2 is crucial for postimplantation development, and coincides with redistribution of EZH2-dependent histone H3 lysine 27 trimethylation (H3K27me3). Loss of G9a or EZH2 results in upregulation of distinct gene sets involved in processes such as cell cycle regulation as well as germline and embryonic development. Accumulation of H3K9me2 not only occurs at promoters and gene bodies, but also extends to active enhancer elements to promote their developmentally-linked silencing. This epigenetic mechanism is important for priming gene regulatory networks in epiblast cells undergoing rapid cell proliferation in preparation for critical cell fate decisions. Examination of 2 histone modification in 3 cell types and transcriptional analysis of G9a and Ezh2 KO epiblasts and Whole genome bisulfite sequencing in two cell types

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Transcriptome assay of maternal mRNA degradation in ERK-deleted oocytes

Project description:We analyzed the functions of ERK in maternal mRNA degradation in mouse oocytes. By comparing the degradation of transcripts in WT oocytes and KO oocytes, we are able to know the defects in maternal mRNA clearance in ERK-deleted oocytes, and identified the ERK target genes in oocyte maturation.

2016-12-16 | GSE92317 | GEO

The genomic distribution of G9a, H3K9me2, H3K27me3 and Mef2c in cardiomyocyte-enriched populations isolated from G9a-KO and Cre mice

Project description:The role of the histone methyltrasferase G9a (also known as Ehmt2) in the normal heart has not been studied extensively. To identify the genomic regions bound to G9a in cardiomyocytes (CMs),we first generated a conditional, cardiac-specific KO mouse for this gene using the Cre-Lox approach, crossing G9a flox/flox mice with αMHC-MerCreMer mice (Cre mice were used as controls). Then we performed ChIP-seq for G9a and H3K9me2 – the main histone methylation catalysed by the HMT – on isolated G9a-KO and Cre CMs, and considered the best G9a-bound genomic regions as those that had a loss or decrease of G9a binding as well as a lower level of H3K9me2 in G9a-KO CMs. Since G9a contributes to trimethylation of H3K27 at a set of developmental genes through its interaction with PRC2, we also evaluated whether the loss of G9a had an effect on the distribution of this histone mark. To this end, we performed ChIP-seq for H3K27me3 in Cre CMs and G9a-KO CMs. Finally co-immunoprecipitation assays revealed that G9a interacts with Mef2c, thus to elucidate the function of the G9a–Mef2c interaction in adult cardiomyocytes, we used ChIP-seq to define the genomic distribution of Mef2c in Cre CMs and G9a-KO CMs.

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Transcriptome assay of materal mRNA degradation in Btg4-deleted oocytes

Project description:We analyzed the functions of BTG family proteins in maternal mRNA degradation in mouse oocytes. By comparing the degradation of transcripts in WT oocytes and KO oocytes, we are able to know the defects in maternal mRNA clearance in BTG4-deleted oocytes, and identified the BTG4 target genes in oocyte cyplasmic maturation.

2016-03-16 | GSE71257 | GEO

Mammalian oocytes store proteins in cytoplasmic lattices

Project description:Oocytes must accumulate and store maternal factors such as proteins during growth to sustain the first stages of embryonic development. How mammalian oocytes store maternal proteins is not understood. Here, we show that mouse and human oocytes store proteins on cytoplasmic lattices. With super-resolution light microscopy and electron tomography, we demonstrate that cytoplasmic lattices are twisted filament bundles formed by proteins of the subcortical maternal complex, filling the entire ooplasm. The lattices were associated with many proteins that have crucial functions during early embryo development, including proteins controlling genome methylation. Loss of cytoplasmic lattices prevented the accumulation of these proteins and resulted in early embryonic arrest. Thus, cytoplasmic lattices are important for storage of essential maternal proteins and the developmental success of early mammalian embryos.

2023-10-23 | PXD038575 | Pride

Sirena1: The most abundant lncRNA in mouse oocytes brings together post-transcriptional regulations and mitochondrial distribution (rat wild-type GV oocytes)

Project description:Long non-coding RNAs (lncRNAs) are a large group of rapidly evolving non-coding RNAs. Tens of thousands of lncRNAs were identified but function has been assigned to relatively few. LncRNAs expressed in mouse oocytes have been annotated but their contribution to oocyte development and early development remains unknown. Here, we report evolutionary history and functional analysis of Sirena1, maternal lncRNA that is the most expressed maternal lncRNA and 10th most abundant Pol II transcript in mouse oocytes.

2019-09-30 | GSE137562 | GEO

Regulation of mammalian 3D genome organization and histone H3K9 dimethylation by H3K9 methyltransferases

Project description:Histone H3 lysine 9 dimethylation (H3K9me2) is a highly conserved silencing epigenetic mark. Chromatin marked with H3K9me2 forms large domains in mammalian cells and overlaps well with lamina-associated domains and the B compartment defined by Hi-C. However, the role of H3K9me2 in 3-dimensional (3D) genome organization remains unclear. We investigated genome-wide H3K9me2 distribution, transcriptome, and 3D genome organization in mouse embryonic stem cells following the inhibition or depletion of five H3K9 methyltransferases (MTases): G9a, GLP, SETDB1, SUV39H1, and SUV39H2. H3K9me2 was regulated by all five MTases; however, H3K9me2 and transcription in the A and B compartments were regulated by different MTases. H3K9me2 in A compartments was primarily regulated by G9a/GLP and SETDB1, while H3K9me2 in the B compartments was regulated by all five MTases. Furthermore, decreased H3K9me2 correlated with changes to the more active compartmental state that accompanied transcriptional activation.

2021-08-05 | PXD024756 | Pride

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