Genome-wide methylation profile of mitochondrial DNA across bovine preimplantation development
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ABSTRACT:
PROVIDER: PRJNA961670 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24299119_1.fastq.gz | Fastqsanger.gz | |||
| SRR24299119_2.fastq.gz | Fastqsanger.gz | |||
| SRR24299120_1.fastq.gz | Fastqsanger.gz | |||
| SRR24299120_2.fastq.gz | Fastqsanger.gz | |||
| SRR24299121_1.fastq.gz | Fastqsanger.gz |
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Project description:This study characterized variations in the methylation profile of mitochondrial DNA (mtDNA) during initial bovine embryo development and correlated the presence of methylation with mtDNA transcription. Bovine oocytes were obtained from abattoir ovaries and submitted to in vitro culture procedures. Oocytes and embryos were collected at various stages (immature oocyte, IM; mature oocyte, MII; zygote, ZY; 4-cells, 4C; 16-cells, 16C and blastocysts, BL). Total DNA (including mtDNA) was used for Whole Genome Enzymatic Methyl Sequencing and for quantification of mtDNA copy number. Extracted RNA was used for quantification of mitochondrial transcripts (ND6, CYTB, tRNA-Phe and tRNA-Gln) using Droplet Digital PCR. The number of mtDNA copies per oocyte/embryo was found to be similar, while methylation levels in mtDNA varied among stages. Higher total methylation levels were found mainly at 4C and 16C. In specific gene regions, higher methylation levels were also observed at 4C and 16C (ND6, CYTB and tRNA-Phe), as well as an inverse correlation with the quantity of transcripts for these regions. This is a first description of epigenetic changes occurring in mtDNA during early embryonic development. Our results indicate that methylation might regulate the mtDNA transcription at a local level, particularly around the time of embryonic genome activation.
2024-04-24 | GSE230476 | GEO
Project description:This study characterized variations in the methylation profile of mitochondrial DNA (mtDNA) during initial bovine embryo development and correlated the presence of methylation with mtDNA transcription. Bovine oocytes were obtained from abattoir ovaries and submitted to in vitro culture procedures. Oocytes and embryos were collected at various stages (immature oocyte, IM; mature oocyte, MII; zygote, ZY; 4-cells, 4C; 16-cells, 16C and blastocysts, BL). Total DNA (including mtDNA) was used for Whole Genome Enzymatic Methyl Sequencing and for quantification of mtDNA copy number. Extracted RNA was used for quantification of mitochondrial transcripts using Droplet Digital PCR. We selected ND6, CYTB, tRNA-Phe and tRNA-Gln based on their location in the mitochondrial genome, functionality and/or previous literature associating these regions with cytosine methylation. The number of mtDNA copies per oocyte/embryo was found to be similar, while methylation levels in mtDNA varied among stages. Higher total methylation levels were found mainly at 4C and 16C. In specific gene regions, higher methylation levels were also observed at 4C and 16C (ND6, CYTB and tRNA-Phe), as well as an inverse correlation with the quantity of transcripts for these regions. This is a first description of epigenetic changes occurring in mtDNA during early embryonic development. Our results indicate that methylation might regulate the mtDNA transcription at a local level, particularly around the time of embryonic genome activation.
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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.
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Project description:This study provides the first comprehensive analysis of gene expression and transcriptome dynamics of bovine metaphase II oocytes and in vivo developing bovine embryos. For this study, Affymetrix GeneChip Bovine Genome Array which covers ~23,000 transcripts was used, which revealed several distinct clusters of genes regulated during various stages of bovine preimplantation development. Keywords: Time course
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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.
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Project description:Maternal nutrition exclusively during the periconceptional period can induce remarkable effects on both oocyte maturation and early embryo development, which in turn can have lifelong consequences. The objective of this study was to evaluate the effect of maternal methionine supplementation on the transcriptome of bovine preimplantation embryos. Holstein cows were randomly assigned to one of two treatments differing in level of dietary methionine (1.89 Met vs. 2.43 Met % of metabolizable protein) from calving until embryo flushing. High quality preimplantation embryos from individual cows were pooled and then analyzed by RNA sequencing.
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Project description:Maternal nutrition exclusively during the periconceptional period can induce remarkable effects on both oocyte maturation and early embryo development, which in turn can have lifelong consequences. The objective of this study was to evaluate the effect of maternal methionine supplementation on the transcriptome of bovine preimplantation embryos. Holstein cows were randomly assigned to one of two treatments differing in level of dietary methionine (1.89 Met vs. 2.43 Met % of metabolizable protein) from calving until embryo flushing. High quality preimplantation embryos from individual cows were pooled and then analyzed by RNA sequencing. A total of eight Holstein dairy cows were used in this study. Preimplantation embryos recovered from each cow were pooled in order to generate two replicates per cow assayed. Each pool consisted of 2-4 expanded blastocysts with excellent quality. Overall, a total of 16 embryo pools underwent RNA extraction, amplification, and subsequent sequencing.
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Project description:The objective of this study was to identify changes on the CSF2 embryo transcriptome that make them more able to become a blastocyst and more likely to survive after transfer. Embryos were treated with CSF2 at day 5 after fertilization and at day 6 morulae and blastocysts were select for the microarray analysis. A total of 160 genes that had a 1.5-fold difference in expression and a significance of P M-bM-^IM-$ 0.05 could be annotated. Analysis of the data identified 13 biological process ontologies that could be grouped into four functional groups (development and differentiation process, cell communication, apoptosis and cell adhesion). Experimental conditions: CSF2 treated vs. CSF2 nontreated bovine in vitro produced preimplantation embryos. Biological replicates: CSF2 treated vs. nontreated bovine preimplantation embryos were used in a dye switch two-color microarray experimental design. Ratio data was not used in these experiments.
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