Chromatin remodeling in bovine embryos indicates species-specific regulation of genome activation
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA601200 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Characterization of genome-wide chromatin accessibility in bovine oocytes and preimplantation embryos using ATAC-seq
2020-05-05 | GSE143658 | GEO
Project description: Not available
| S-EPMC7498599 | biostudies-literature
Project description:Profiles of H3K4me3, H3K27ac, H3K27me3 and H3K9me3 in bovine GV oocytes and preimplantation embryos, and the characterization of chromatin accessibility in bovine blastocyst, inner cell mass and trophectoderm.
2023-02-16 | GSE193640 | GEO
Project description:Affymetrix Human GeneChips are used to profile gene expression of bovine tissues and embryos to identify uniquely expressed genes in bovine in-vitro fertilized embryos by comparing with seven bovine adult tissues through gene clustering Keywords: other
2004-08-05 | GSE1638 | GEO
Project description:Proper lineage specification is extremely important for the embryo's implantation and development. Numerous findings of lineage specification emerged in the mouse embryo but remain unclear in the bovine embryo due to the limited techniques. Here, our study is the first to demonstrate that the single base editor (ABE7.10 and BE3) can be applied to bovine embryos for base conversion, which contributes us to further exploring the lineage specification of the bovine embryo. We further show SOX2 is not necessary for blastocyst formation but is required for ICM maintenance in bovine early embryo development. The underlying mechanism may be that SOX2 promoted the differentiation of ICM by maintaining the expression levels of OCT4 and NANOG. Meanwhile, the disappearance of SOX2 in TE of bovine late blastocyst depended on the expression of CDX2.
2022-03-22 | GSE189318 | GEO
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:During maternal-to-embryonic transition control of embryonic development gradually switches from maternal RNAs and proteins stored in the oocyte to gene products generated after embryonic genome activation (EGA). Detailed insight into the onset of embryonic transcription is obscured by the presence of maternal transcripts. Using the bovine model system, we established by RNA sequencing a comprehensive catalogue of transcripts in germinal vesicle and metaphase II oocytes, and in embryos at the 4-cell, 8-cell, 16-cell and blastocyst stages. These were produced by in vitro fertilization of Bos t. taurus oocytes with sperm from a Bos t. indicus bull to facilitate parent-specific transcriptome analysis. Transcripts from 12.4 to 13.7 M-CM-^W 10^3 different genes were detected in the various developmental stages. EGA was analyzed by i) detection of embryonic transcripts which are not present in oocytes; ii) detection of transcripts from the paternal allele; and iii) detection of primary transcripts with intronic sequences. These strategies revealed (i) 220, (ii) 937, and (iii) 6,848 genes to be activated from the 4-cell to the blastocyst stage. The largest proportion of gene activation, i.e. (i) 59%, (ii) 42%, and (iii) 58%, was found in 8-cell embryos, indicating major EGA at this stage. Gene ontology analysis of genes activated at the 4-cell stage identified categories related to translation, RNA processing and transport, consistent with preparation for major EGA. Our study provides the largest transcriptome data set of bovine oocyte maturation and early embryonic development and new insight into the timing of embryonic activation of specific genes. RNA-Seq profiles from pools of 10 ooytes/embryos from bovine Bos t. taurus GV and MII oocytes and a cross-breed of Bos t. taurus x Bos t. indicus from 4-cell, 8-cell, 16-cell and blastocysts generated using Illumina GAIIx
2014-02-09 | E-GEOD-52415 | biostudies-arrayexpress
Project description:Global hypermethylations of histone H3 lysine 9 (H3K9) tri- and di-methylation (H3K9me3/2) have been identified in bovine cloned embryos at the embryonic genome activation (EGA) stage (eight-cell stage), but the intrinsic reason for these anomalies remains elusive. To ascertain key factors responsible for aberrant H3K9 methylation, we performed RNA sequencing of transcripts in eight-cell bovine in vitro fertilized (IVF) and SCNT embryo. From the differentially expressed genes (DEGs) between IVF and SCNT embryos, we identified that the unsuccessful reactivation of two histone demethylases, KDM4D and KDM4E, is responsible for the incomplete H3K9me3/2 demethylation in SCNT embryos at the EGA stage. By mRNA injection, ectopic expression of either KDM4D or KDM4E could erase H3K9me3/2 barriers, improve blastocyst formation, and elevate cloning efficiency of bovine SCNT. To examine the detailed genes responsive to KDM4E overexpression, we also performed RNA sequencing of bovine eight-cell SCNT embryos with KDM4E compensation and found an obvious restoration of global transcriptional patterns in SCNT embryos. Our study first provides the transcriptome data set of bovine IVF and SCNT embryos during EGA with or without KDM4E overexpression, which advance the understanding of incomplete nuclear reprogramming, and contribute to the practical implications for genetically modified livestock breeding using SCNT.
2018-01-16 | GSE99294 | GEO
Project description:During maternal-to-embryonic transition control of embryonic development gradually switches from maternal RNAs and proteins stored in the oocyte to gene products generated after embryonic genome activation (EGA). Detailed insight into the onset of embryonic transcription is obscured by the presence of maternal transcripts. Using the bovine model system, we established by RNA sequencing a comprehensive catalogue of transcripts in germinal vesicle and metaphase II oocytes, and in embryos at the 4-cell, 8-cell, 16-cell and blastocyst stages. These were produced by in vitro fertilization of Bos t. taurus oocytes with sperm from a Bos t. indicus bull to facilitate parent-specific transcriptome analysis. Transcripts from 12.4 to 13.7 × 10^3 different genes were detected in the various developmental stages. EGA was analyzed by i) detection of embryonic transcripts which are not present in oocytes; ii) detection of transcripts from the paternal allele; and iii) detection of primary transcripts with intronic sequences. These strategies revealed (i) 220, (ii) 937, and (iii) 6,848 genes to be activated from the 4-cell to the blastocyst stage. The largest proportion of gene activation, i.e. (i) 59%, (ii) 42%, and (iii) 58%, was found in 8-cell embryos, indicating major EGA at this stage. Gene ontology analysis of genes activated at the 4-cell stage identified categories related to translation, RNA processing and transport, consistent with preparation for major EGA. Our study provides the largest transcriptome data set of bovine oocyte maturation and early embryonic development and new insight into the timing of embryonic activation of specific genes.
2014-02-09 | GSE52415 | GEO
Project description:Dynamic changes in DNA methylation are crucial in the epigenetic regulation of mammalian embryogenesis. Global DNA methylation studies in the bovine, however, remain mostly at the immunostaining level. We adopted the single-cell whole genome bisulfite sequencing (scWGBS) method to characterize stage-specific genome-wide DNA methylation in bovine sperm, individual oocytes derived in vivo and in vitro, as well as in vivo developed embryos at the 2-, 4-, 8- and 16-cell stages. This method allowed us to theoretically cover all CpG sites in the genome using single oocytes or embryos. We found that the major wave of genome-wide DNA demethylation was complete at the 8-cell stage when de novo methylation became prominent. Sperm and oocytes were differentially methylated in numerous regions (DMRs) which were enriched in intergenic regions, indicating these noncoding regions play important roles in gamete specification. DMRs were also identified between in vivo and in vitro matured oocytes. Moreover, X chromosome methylation followed the global dynamic patterns. Virtually no (less than 1.5%) DNA methylation was found in mitochondrial DNA. Finally, using our RNA-seq data generated from the same developmental stages, we revealed an inverse correlation between gene expression and promoter methylation. Our study provides the first fully comprehensive analysis of the global dynamics of DNA methylation in bovine gametes and single early embryos using scWGBS. These data provide insights into the critical features of the methylome of bovine embryos, and serve as an important reference for embryos produced by assisted reproduction, such as in vitro fertilization and cloning, and a model for human early embryo epigenetic regulation.
2019-05-13 | GSE121758 | GEO