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DNA methylation changes during preimplantation development reveal inter species-differences and reprogramming events at imprinted genes [RNA-Seq]

ABSTRACT: DNA methylation changes during preimplantation development reveal inter species-differences and reprogramming events at imprinted genes [RNA-Seq]

PROVIDER: PRJNA601900 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10907220.fastq.gz	Fastqsanger.gz
	SRR10907221.fastq.gz	Fastqsanger.gz
	SRR10907222.fastq.gz	Fastqsanger.gz
	SRR10907223.fastq.gz	Fastqsanger.gz
	SRR10907224.fastq.gz	Fastqsanger.gz

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DNA methylation changes during preimplantation development reveal inter species-differences and reprogramming events at imprinted genes

Project description:DNA methylation changes during preimplantation development reveal inter species-differences and reprogramming events at imprinted genes

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DNA methylation changes during preimplantation development reveal inter species-differences and reprogramming events at imprinted genes [BS-Seq]

Project description:DNA methylation changes during preimplantation development reveal inter species-differences and reprogramming events at imprinted genes [BS-Seq]

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DNA methylation changes during preimplantation development reveal inter species-differences and reprogramming events at imprinted genes [BS-Seq]

Project description:Preimplantation embryos experience profound resetting of epigenetic information. Genome-wide analysis at single-base resolution had shown relevant species differences between human and mouse preimplantation embryos. Thus, we have extended such analysis to two key livestock species, the pig and the cow. We generated data showing the genome-wide DNA methylation landscape and whole-transcriptomes from gametes to blastocysts in both species. Detailed analysis revealed species specific differences and new insights in biological paradigms. An oocyte-like pattern of methylation in the cleavage stages, albeit with some reduction in methylation level, appears to persist even in cow blastocysts. Hypermethylated domains were prevalent over hypomethylated domains in pigs and cows, similar to human, while in the mouse the pattern is reversed. Interestingly, the behaviour of the oocyte hypo-domains in cleavage embryos revealed a complex dynamic of methylation reprogramming. It shows a pronounced increase in methylation at the 8-16 cell stage in pigs, similar to human, concomitant with ZFP57 expression. Even it is widely accepted that imprinted genes are established in the parental germline and robustly maintained through early development, our data show a greater dynamic of methylation in germline differentially methylated regions and few appear to maintain the expected 50% methylation from the 2-4 cell stage to blastocyst stage. It reveals that an active period of imprint stabilization until the blastocyst stage is required

2020-05-20 | GSE143849 | GEO

DNA methylation changes during preimplantation development reveal inter species-differences and reprogramming events at imprinted genes [RNA-Seq]

2020-05-20 | GSE143848 | GEO

DNA methylation changes during preimplantation development reveal inter-species differences and reprogramming events at imprinted genes.

Project description:Preimplantation embryos experience profound resetting of epigenetic information inherited from the gametes. Genome-wide analysis at single-base resolution has shown similarities but also species differences between human and mouse preimplantation embryos in DNA methylation patterns and reprogramming. Here, we have extended such analysis to two key livestock species, the pig and the cow. We generated genome-wide DNA methylation and whole-transcriptome datasets from gametes to blastocysts in both species. In oocytes from both species, a distinctive bimodal methylation landscape is present, with hypermethylated domains prevalent over hypomethylated domains, similar to human, while in the mouse the proportions are reversed.An oocyte-like pattern of methylation persists in the cleavage stages, albeit with some reduction in methylation level, persisting to blastocysts in cow, while pig blastocysts have a highly hypomethylated landscape. In the pig, there was evidence of transient de novo methylation at the 8-16 cell stages of domains unmethylated in oocytes, revealing a complex dynamic of methylation reprogramming. The methylation datasets were used to identify germline differentially methylated regions (gDMRs) of known imprinted genes and for the basis of detection of novel imprinted loci. Strikingly in the pig, we detected a consistent reduction in gDMR methylation at the 8-16 cell stages, followed by recovery to the blastocyst stage, suggesting an active period of imprint stabilization in preimplantation embryos. Transcriptome analysis revealed absence of expression in oocytes of both species of ZFP57, a key factor in the mouse for gDMR methylation maintenance, but presence of the alternative imprint regulator ZNF445. In conclusion, our study reveals species differences in DNA methylation reprogramming and suggests that porcine or bovine models may be closer to human in key aspects than in the mouse model.

| S-EPMC7216732 | biostudies-literature

DNA methylation changes during preimplantation development reveal inter species-differences and reprogramming events at imprinted genes

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

2020-05-20 | GSE143850 | GEO

Correction to: DNA methylation changes during preimplantation development reveal interspecies differences and reprogramming events at imprinted genes.

Project description:An amendment to this paper has been published and can be accessed via the original article.

| S-EPMC7322833 | biostudies-literature

Maternal SMCHD1 controls both imprinted Xist expression and imprinted X chromosome inactivation

Project description:Embryonic development is dependent on the maternal supply of proteins through the oocyte, including factors setting up the adequate epigenetic patterning of the zygotic genome. We previously reported that one such factor is the epigenetic repressor SMCHD1, whose maternal supply controls autosomal imprinted expression in mouse preimplantation embryos and mid-gestation placenta. In mouse preimplantation embryos, X chromosome inactivation is also an imprinted process. Combining genomics and imaging, we show that maternal SMCHD1 is required not only for the imprinted expression of Xist in preimplantation embryos, but also for the efficient silencing of the inactive X in both the preimplantation embryo and mid-gestation placenta. These results expand the role of SMCHD1 in enforcing the silencing of Polycomb targets. The inability of zygotic SMCHD1 to fully restore imprinted X inactivation further points to maternal SMCHD1's role in setting up the appropriate chromatin environment during preimplantation development, a critical window of epigenetic remodelling.

2021-10-24 | GSE186315 | GEO

Metabolic control of DNA methylation and imprinted gene expression in naive pluripotent cells

Project description:Naive pluripotent epiblast cells of the preimplantation murine embryo and their in vitro counterpart, embryonic stem (ES) cells, have the capacity to give rise to all cells of the adult. Such developmental plasticity is associated with global genome hypomethylation. It is unclear whether genome methylation is dynamically regulated only via differential expression of DNA methyltransferases (DNMTs) and Ten-eleven Translocation (TET) enzymes, which oxidase methylated DNA. Here we show that LIF/Stat3 signalling induces genomic hypomethylation via metabolic reconfiguration. In Stat3-/- ES cells we observed decreased alpha-ketoglutarate (ɑKG) production from reductive Glutamine metabolism, leading to decreased TET activity, increased Dnmt3a/b expression and to a global increase in DNA methylation. Notably, genome methylation is dynamically controlled by simply modulating αKG availability, mitochondrial activity or Stat3 activation in mitochondria, indicating effective crosstalk between metabolism and the epigenome. Stat3-/- ES cells also show increased methylation at Imprinting Control Regions accompanied with differential expression of >50% of imprinted genes. Single-cell transcriptome analysis of Stat3-/- embryos confirmed dysregulated expression of Dnmt3a/b, Tet2, and imprinted genes in vivo. Our results reveal that the LIF/Stat3 signal bridges the metabolic and epigenetic profiles of naive pluripotent cells, ultimately controlling genome methylation and imprinted gene expression. Several imprinted genes regulate cell proliferation and are often misregulated in tumors. Moreover, a wide range of cancers display Stat3-overactivation, raising the possibility that the molecular module we described here is exploited under pathological conditions.

2020-11-26 | PXD020385 | Pride

Trunk events present minimal intra- and inter-tumoral heterogeneity in hepatocellular carcinoma

Project description:Trunk events present minimal intra- and inter-tumoral heterogeneity in hepatocellular carcinoma

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