Ontology highlight
ABSTRACT:
PROVIDER: PRJNA818321 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18399624.fastq.gz | Fastqsanger.gz | |||
| SRR18399625.fastq.gz | Fastqsanger.gz | |||
| SRR18399626.fastq.gz | Fastqsanger.gz | |||
| SRR18399627.fastq.gz | Fastqsanger.gz | |||
| SRR18399628.fastq.gz | Fastqsanger.gz |
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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:Epigenetic markers, such as DNA methylation, in sperm plays crucial roles in spermatogenesis and fertilization, and a portion of methylation escape the early embryonic genome-wide DNA demethylation and affect later growth and development of offspring. DNA methylation is influenced by various exogenous factors such as nutrition, temperature, toxicants, and stress. The effects of this cold exposure on the methylation dynamics of bovine sperm remain unexamined. Methylation profiles of sperm, collected from bulls during summer and winter seasons were analyzed by Whole Genome Bisulfite Sequencing (WGBS). Cold exposure during winter does not have a significant effect on the global methylation level, it altered the methylation levels at certain genomic loci and genes that may impact the maintenance of methylation status of imprinted genes and other loci, which may impact the development and growth of offspring.
2024-01-31 | GSE222863 | GEO
Project description:Sperm carries information to the presumptive embryo upon fertilization in terms of epigenetic codes and transcripts along with the haploid genome. The epigenetic code includes DNA methylation and histone modifications. During spermatogenesis, the DNA of sperm undergoes overall methylation changes and this could have some role to play in fertilizing ability of the sperm. Many of the studies have shown that the altered methylation can cause sub fertility. In the present study we report the development of first comprehensive 4X180K buffalo (Bubalus bubalis) CpG island/promoter microarray for studying the global DNA methylation profile of buffalo sperm. The array has been developed by employing microarray based comparative genomic hybridization (aCGH) technique with bovine and buffalo DNA using bovine genome sequence as reference. The array represents 157084 features assembled from CDS, Promotor and CpG regions covering 2,967 unique genes. We also report the comparison of genome wide methylation differences in buffalo sperm from high fertile and sub fertile bulls which indicated profound discrepancies in their methylation status. A total of 96 individual genes along with another 55 genes covered under CpG islands were found differentially methylated and and were associated with different cellular functions and biological processes affecting germ cell development, spermatogenesis, capacitation and embryonic development.
2014-12-24 | GSE46460 | 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
Project description:DNA from expanded bovine blastocysts and bovine sperm were extracted then subjected to methylation-sensitive enzymatic digestion and LM-PCR enrichment before being hybridized onto a microarray.
2014-09-09 | GSE57709 | GEO
Project description:DNA from expanded bovine blastocysts and bovine sperm were extracted then subjected to methylation-sensitive enzymatic digestion and LM-PCR enrichment before being hybridized onto a microarray. Two-condition experiment, bovine blastocysts (pools of 10) vs bovine sperm. Four biological replicates of each tissue were hybridized to four two-color arrays in a dye-balanced design.
2014-09-09 | E-GEOD-57709 | biostudies-arrayexpress
Project description:Sperm cells are characterized by a unique epigenome, and an incorrect establishment of DNA methylation patterns during the differentiation of male germ cells into spermatozoa has been associated with male infertility in several species. While bull semen is widely used in artificial insemination, the literature describing DNA methylation in bovine sperm is still scarce. The purpose of this study is to compare the methylomes of sperm and somatic cell types in cattle using the RRBS technology.
2018-05-03 | GSE102169 | GEO
Project description:Comparison of the DNA methylation of bovine blastocysts and bovine sperm
| PRJNA248020 | ENA
Project description:Sperm cells are characterized by a unique epigenome, and an incorrect establishment of DNA methylation patterns during the differentiation of male germ cells into spermatozoa has been associated with male infertility in several species. While bull semen is widely used in artificial insemination, the literature describing DNA methylation in bovine sperm is still scarce. The purpose of this study is to compare the methylomes of sperm and somatic cell types in cattle using the MeDIP-chip technology (methylated DNA immunoprecipitation followed by microarray hybridation).
2018-05-03 | GSE102960 | GEO
Project description:We report the application of whole genome bisulfite sequencing technology for high-throughput profiling of DNA methylation in mice sperm at young and aging stages. By obtaining over 500 billion bases of sequence from genomic DNA, we generated genome-wide methylation-state maps of sperm from young and aging stages. We find that 2984 differetial methylation regions(DMR) in whole genome, including 916 DMR in promoter regions betweenin sperm from young and aging stages. 591 of DMR in promoter regions were significantly hypomethylated (~59.82%) and 397 significantly hypermethylated (~40.18%) in sperm of old males.
2022-11-28 | GSE141249 | GEO