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SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development [RNA-seq]

ABSTRACT: SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development [RNA-seq]

PROVIDER: PRJNA449120 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6956490_1.fastq.gz	Fastqsanger.gz
	SRR6956490_2.fastq.gz	Fastqsanger.gz
	SRR6956491_1.fastq.gz	Fastqsanger.gz
	SRR6956491_2.fastq.gz	Fastqsanger.gz
	SRR6956492_1.fastq.gz	Fastqsanger.gz

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SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development [ChIP-seq]

Project description:The oocyte epigenome plays critical roles in mammalian gametogenesis and embryogenesis. Yet, how it is established remains elusive. Here, we report that histone-lysine N-methyltransferase SETD2, an H3K36me3 methyltransferase, is a crucial regulator of the mouse oocyte epigenome. Deficiency in Setd2 leads to extensive alterations of the oocyte epigenome, including the loss of H3K36me3, failure in establishing the correct DNA methylome, invasion of H3K4me3 and H3K27me3 into former H3K36me3 territories and aberrant acquisition of H3K4me3 at imprinting control regions instead of DNA methylation. Importantly, maternal depletion of SETD2 results in oocyte maturation defects and subsequent one-cell arrest after fertilization. The preimplantation arrest is mainly due to a maternal cytosolic defect, since it can be largely rescued by normal oocyte cytosol. However, chromatin defects, including aberrant imprinting, persist in these embryos, leading to embryonic lethality after implantation. Thus, these data identify SETD2 as a crucial player in establishing the maternal epigenome that in turn controls embryonic development.

2019-05-01 | GSE112834 | GEO

SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development [Bisulfite-seq]

2019-05-01 | GSE112833 | GEO

SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development [RNA-seq]

2019-05-01 | GSE112832 | GEO

SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development

Project description:SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development

| PRJNA449119 | ENA

SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development [ChIP-seq]

Project description:SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development [ChIP-seq]

| PRJNA449122 | ENA

SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development [Bisulfite-seq]

Project description:SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development [Bisulfite-seq]

| PRJNA449121 | ENA

Genomic imprinting of Xist by maternal H3K27me3

Project description:Maternal imprinting at the Xist gene is essential to achieve paternal allele-specific imprinted X chromosome inactivation (XCI) in female mammals. However, the mechanism underlying the Xist imprinting is unclear. Here we show that the Xist gene is coated with H3K27me3 in mouse oocytes, which persists through preimplantation development. Ectopic removal of H3K27me3 induces maternal Xist expression and maternal XCI, indicating that maternal H3K27me3 is the imprinting mark of Xist.

2017-11-09 | GSE103714 | GEO

SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development

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

2019-05-01 | GSE112835 | GEO

Maternal Eed knockout causes loss of H3K27me3 imprinting and random X-inactivation in the extra-embryonic cells

Project description:Genomic imprinting is essential for mammalian development. Recent studies have revealed that maternal histone H3 lysine 27 tri-methylation (H3K27me3) can mediate DNA methylation-independent genomic imprinting. However, the regulatory mechanisms and functions of this new imprinting mechanism are largely unknown. Here we demonstrate that maternal Eed, an essential component of the Polycomb group complex 2 (PRC2), is required for establishing H3K27me3 imprinting. We found that all H3K27me3 imprinted genes, including Xist, lose their imprinted expression in Eed maternal KO (matKO) embryos, resulting in male-biased lethality. Surprisingly, although maternal X chromosome inactivation (XmCI) occurs in Eed matKO embryos at preimplantation due to loss of Xist imprinting, it is resolved at peri-implantation. Ultimately, both X chromosomes are reactivated in the embryonic cell lineage prior to random XCI, and only a single X chromosome undergoes random XCI in the extra-embryonic cell lineage. Thus, our study not only demonstrates an essential role of Eed in H3K27me3 imprinting establishment but also reveals a unique XCI dynamics in the absence of Xist imprinting.

2018-11-26 | GSE116713 | GEO

Effects of Maternal Energy Intake on Genomic Imprinting in Fetal Sheep

Project description:Background: Genomic imprinting is an epigenetic phenomenon of differential allelic expression based on parental origin. To date a total of 255 imprinted genes have been identified or predicted among all investigated mammal species. However, only 21 have been described in sheep and 11 are annotated in current ovine genome. Results: Here we aim to use DNA/RNA throughput sequencing to identify monoallelically expressed and imprinted genes in organs of day 135 fetal sheep, and 2) to determine whether different levels of maternal energy intake (100% of NRC energy requirement or control, 140% or over-, and 60% or under-fed) influence genomic imprinting. We report strategies to solve technical challenges in the next-generation sequencing data analysis pipeline, including alignment bias of RNA sequencing reads and filtering potential false positives. We identified 80 monoallelically expressed and 18 putatively imprinted genes using the list of 255 stated above as a guide. Five (45.6% of 11) were already known imprinted genes in sheep, the other 13 were known imprinted in other mammals. Sanger sequencing confirmed four putative sheep imprinted genes INPP5F, PLAGL1, CASD1 and PPP1R9A. Among the 13 putative imprinted genes, five localized in the known sheep imprinting clusters of MEST domain on chromosome 4, DLK1/GTL2 domain on chromosome 18 and IGF2/H19 domain on chromosome 21, three were in a novel sheep imprinted cluster on chromosome 4 known in other species as PEG10/SGCE. Additionally, we found that the imprinted genes PHLDA2, SLC22A18, DIRAS3, and IGF2 were differentially expressed, albeit without allelic expression reversal, among the three maternal nutritional groups. Conclusions: Together, our results expanded the sheep imprinted gene list to 34 and demonstrated the influence of maternal diet on fetal imprinting under the conditions studied.

2018-08-29 | GSE111306 | GEO

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