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Single-cell transcriptome analysis of uniparental embryos reveals parent-of-origin effects on human preimplantation development [RNA-seq]

ABSTRACT: Single-cell transcriptome analysis of uniparental embryos reveals parent-of-origin effects on human preimplantation development [RNA-seq]

PROVIDER: PRJNA552818 | ENA |

REPOSITORIES: ENA

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Single-cell transcriptome analysis of uniparental embryos reveals parent-of-origin effects on human preimplantation development [methylation]

Project description:To investigate the contribution of parental genomes to early embryogenesis, we systematically profiled the single-cell transcriptomes of human biparental and uniparental embryos from one-cell to morula stages. We observed that uniparental embryos exhibit variable and overall less activation patterns of embryonic genome activation (EGA). Comparative transcriptome analysis identified 807 maternally biased expressed genes (MBGs) and 581 paternally biased expressed genes (PBGs) in preimplantation stages. MBGs became obviously appeared at the four-cell stage and contribute to EGA initiation, whereas PBGs preferentially appeared at the eight-cell stage, and possibly affect embryo compaction and trophectoderm specification. Regulatory network analysis revealed DUX4, EGR2 and DUXA as key transcription factors for MBGs expression as well as ZNF263 and KLF3 for PBGs expression. Furthermore, we revealed that the expression of MBGs and PBGs，especially PBGs, probably due to DNA methylation differences between the parental genomes. Together, our results provide a valuable resource to understand parental genome activation and may help to dissect parent-of-origin effect on early human development.

2019-10-08 | GSE133855 | GEO

Single-cell transcriptome analysis of uniparental embryos reveals parent-of-origin effects on human preimplantation development [RNA-seq]

Project description:To investigate the contribution of parental genomes to early embryogenesis, we systematically profiled the single-cell transcriptomes of human biparental and uniparental embryos from one-cell to morula stages. We observed that uniparental embryos exhibit variable and overall less activation patterns of embryonic genome activation (EGA). Comparative transcriptome analysis identified 807 maternally biased expressed genes (MBGs) and 581 paternally biased expressed genes (PBGs) in preimplantation stages. MBGs became obviously appeared at the four-cell stage and contribute to EGA initiation, whereas PBGs preferentially appeared at the eight-cell stage, and possibly affect embryo compaction and trophectoderm specification. Regulatory network analysis revealed DUX4, EGR2 and DUXA as key transcription factors for MBGs expression as well as ZNF263 and KLF3 for PBGs expression. Furthermore, we revealed that the expression of MBGs and PBGs especially PBGs, probably due to DNA methylation differences between the parental genomes. Together, our results provide a valuable resource to understand parental genome activation and may help to dissect parent-of-origin effect on early human development.

2019-10-08 | GSE133854 | GEO

Single-cell transcriptome analysis of uniparental embryos reveals parent-of-origin effects on human preimplantation development

Project description:Single-cell transcriptome analysis of uniparental embryos reveals parent-of-origin effects on human preimplantation development

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Single-cell transcriptome analysis of uniparental embryos reveals parent-of-origin effects on human preimplantation development [methylation]

Project description:Single-cell transcriptome analysis of uniparental embryos reveals parent-of-origin effects on human preimplantation development [methylation]

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Mouse preimplantation imprinting [RNA-seq]

Project description:In mammals, chromatin marks at imprinted genes are asymmetrically inherited from each parent to control gene expression. Many genomic imprints are determined by differentially methylated regions (DMRs), but these have not been comprehensively mapped physically or functionally in mouse preimplantation embryos. We here address this by integrating transcriptomic and epigenomic approaches. Transcriptome analysis of blastocysts from genetically distinguishable crosses identified 106 genes with previously unknown parent-of-origin-specific allelic bias (nBsX genes), and 71 novel imprinted genes with parent-of-origin-specific expression with an allelic ratio of 70:30 or greater (nBiX genes). Uniparental expression of tested nBsX and nBiX transcripts disappeared soon after implantation.

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Project description:In mammals, chromatin marks at imprinted genes are asymmetrically inherited from each parent to control gene expression. Many genomic imprints are determined by differentially methylated regions (DMRs), but these have not been comprehensively mapped physically or functionally in mouse preimplantation embryos. To address this, we measured genome-wide DNA methylation in individual haploid uniparental parthenogenetic haploid (ph) and androgenetic haploid (ah) E3.5 blastocysts by micro-whole-genome bisulfite sequencing (µWGBS). For comparison, we also included ahESC and phESC lines in the analysis.Comparison of DNA methylomes from uniparental blastocysts with those of control blastocysts (produced by intracytoplasmic sperm injection) identified 859 DMRs. Haploid ES cells showed overall erosion of those DMRs, in contrast to diploid ES cells that relatively maintained differential methylation.

2021-03-02 | GSE152105 | GEO

The asynchronous establishment of chromatin 3D architecture between in vitro fertilized and uniparental preimplantation pig embryos

Project description:The asynchronous establishment of chromatin 3D architecture between in vitro fertilized and uniparental preimplantation pig embryos

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Single-cell transcriptome analysis of uniparental embryos reveals parent-of-origin effects on human preimplantation development

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-10-08 | GSE133856 | GEO