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Unique Trophoblast Chromatin Environment Mediated by the PcG Protein SFMBT2 [ChIP-seq]

ABSTRACT: Unique Trophoblast Chromatin Environment Mediated by the PcG Protein SFMBT2 [ChIP-seq]

PROVIDER: PRJNA473701 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7233730_1.fastq.gz	Fastqsanger.gz
	SRR7233730_2.fastq.gz	Fastqsanger.gz
	SRR7233731_1.fastq.gz	Fastqsanger.gz
	SRR7233731_2.fastq.gz	Fastqsanger.gz
	SRR7233732_1.fastq.gz	Fastqsanger.gz

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Unique Trophoblast Chromatin Environment Mediated by the PcG Protein SFMBT2

Project description:Unique Trophoblast Chromatin Environment Mediated by the PcG Protein SFMBT2

| PRJNA483475 | ENA

Unique Trophoblast Chromatin Environment Mediated by the PcG Protein SFMBT2 [ChIP-seq]

Project description:Sfmbt2 is a paternally imprinted gene critical for the establishment and maintenance of trophoblast stem cells in mice (Miri K et al., 2013). Inheritance of a gene trap null allele (Sfmbt2gt/gt) results in embryonic lethality by e12.5 due to reduced numbers in all trophoblast cell types. SFMBT2 is a mammalian Polycomb group protein (PcG) and is assumed to act as a master transcriptional regulator. ChIP-seq was performed against endogenous and FLAG-SFMBT2 in trophoblast stem cells (TSCs) to complement the RNA-seq dataset acquired from extraembryonic tissues of wildtype and Sfmbt2gt/gt mice. We aim to determine the binding profile of SFMBT2 in TSCs and how it contributes to the observed transcriptomic profile.

2019-08-18 | GSE115087 | GEO

Unique Trophoblast Chromatin Environment Mediated by the PcG Protein SFMBT2 [RNA-seq]

Project description:Sfmbt2 is a paternally imprinted gene critical for the establishment and maintenance of trophoblast stem cells in mice (Miri K et al., 2013). Inheritance of a paternal Sfmbt2 gene trap null allele (Sfmbt2gt/gt) results in embryonic lethality by e12.5 due to reduced numbers in all trophoblast cell types. Of note, SFMBT2 is characterized as a Polycomb group (PcG) protein and is assumed to act as a master transcriptional repressor. Through RNA-seq analysis of extraembryonic tissues acquired from both wild-type and Sfmbt2gt/gt embryos, we aim to elucidate differentially expressed genes critical for the dramatic phenotype observed in mutant embryos.

2019-08-18 | GSE117879 | GEO

Unique Trophoblast Chromatin Environment Mediated by the PcG Protein SFMBT2 [RNA-seq]

Project description:Unique Trophoblast Chromatin Environment Mediated by the PcG Protein SFMBT2 [RNA-seq]

| PRJNA483478 | ENA

Unique trophoblast chromatin environment mediated by the PcG protein SFMBT2.

Project description:Stem/progenitor cells are maintained by a chromatin environment, mediated in part by Polycomb group (PcG) proteins, which depress differentiation. The trophoblast-specific PcG protein SFMBT2 is known to be required for maintenance of trophoblast progenitors. Rather than binding to trophoblast-specific genes repressed in TSC, SFMBT2 is concentrated at chromocentres and regions rich in repetitive elements, specifically LINE sequences and major satellites, suggesting that it is involved in higher-order organization of the trophoblast genome. It is also found enriched at a subset of ncRNAs. Comparison of ChIP-seq datasets for other chromatin proteins reveals several stereotypical distribution patterns, suggesting that SFMBT2 interacts with several different types of chromatin complexes specific to the trophoblast lineage.

| S-EPMC6737984 | biostudies-literature

Unique Trophoblast Chromatin Environment Mediated by the PcG Protein SFMBT2

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

2019-08-18 | GSE117880 | GEO

The PcG gene Sfmbt2 is paternally expressed in extraembryonic tissues.

Project description:Genomic imprinting has dramatic effects on placental development, as has been clearly observed in interspecific hybrid, somatic cell nuclear transfer, and uniparental embryos. In fact, the earliest defects in uniparental embryos are evident first in the extraembryonic trophoblast. We performed a microarray comparison of gynogenetic and androgenetic mouse blastocysts, which are predisposed to placental pathologies, to identify imprinted genes. In addition to identifying a large number of known imprinted genes, we discovered that the Polycomb group (PcG) gene Sfmbt2 is imprinted. Sfmbt2 is expressed preferentially from the paternal allele in early embryos, and in later stage extraembryonic tissues. A CpG island spanning the transcriptional start site is differentially methylated on the maternal allele in e14.5 placenta. Sfmbt2 is located on proximal chromosome 2, in a region known to be imprinted, but for which no genes had been identified until now. This possibly identifies a new imprinted domain within the murine genome. We further demonstrate that murine SFMBT2 protein interacts with the transcription factor YY1, similar to the Drosophila PHO-RC.

| S-EPMC2220043 | biostudies-literature

Global changes of H3K27me3 domains and PcG protein distribution in the absence of the PcG recruiters Spps or Pho

Project description:Polycomb group (PcG) proteins maintain the silenced state of key developmental genes in animals, but how these proteins are recruited to specific regions of the genome is still poorly understood. In Drosophila, PcG proteins are recruited to Polycomb response elements (PREs) that include combinations of sites for sequence specific DNA binding “PcG recruiters,” including Pho, Cg, and Spps. To understand their roles in PcG recruitment, we compared Pho-, Cg-, and Spps-binding sites against H3K27me3 and key PcG proteins by ChIP-seq in wild-type and mutant third instar larvae. H3K27me3 in canonical Polycomb domains is decreased after the reduction of any recruiter. Reduction of Spps and Pho, but not Cg, causes the redistribution of H3K27me3 to heterochromatin. Regions with dramatically depleted H3K27me3 after Spps knockout are usually accompanied by decreased Pho binding, suggesting their cooperative binding. PcG recruiters, the PRC2 component E(z), and the PRC1 components Psc and Ph cobind thousands of active genes outside of H3K27me3 domains. This study demonstrates the importance of distinct PcG recruiters for the establishment of unique Polycomb domains. Different PcG recruiters can act both cooperatively and independently at specific PcG target genes, highlighting the complexity and diversity of PcG recruitment mechanisms.

2018-03-07 | GSE102339 | GEO

Deciphering the function of Angiomotin in trophoblast cells

Project description:Trophectoderm-specific expression of Angiomotin (AMOT) in pre-implantation embryos followed by its unique expression in the post-implantation ectoplacental cone that harbors the trophoblast stem cell niche prompted our investigation on the function of AMOT in trophoblast cells. Using the in vitro trophoblast stem cell culture model, we established differentiation dependent up-regulation of AMOT expression in trophoblast cells. To understand the function of AMOT in trophoblast cells mass spectrometry-based proteomic analysis was employed to identify the AMOT interactome within the trophoblast proteome. This approach utilized immunoprecipitation of endogenous AMOT followed by fractionation on SDS-PAGE and subsequently subjecting the tryptic digested excised gel bands to mass spectrometry.

2021-11-03 | PXD019391 | Pride

The Rodent-Specific MicroRNA Cluster within the Sfmbt2 Gene is Imprinted and Essential for Placental Development [miRNA]

Project description:MicroRNAs (miRNAs) represent small noncoding RNAs that are involved in physiologic and developmental processes by negatively regulating expression of target genes. They exist as individual miRNA genes or as polycistronically transcribed gene clusters. The largest miRNA cluster in mice is located in intron 10 of the Sfmbt2 gene, and contains 72 miRNA precursor sequences within approximately 50 kb. Although this miRNA cluster emerged recently in the rodent genome, probably coincidentally with the acquisition of the imprinted control of Sfmbt2, very little is known about its functions. In this study, we generated mice lacking the entire Sfmbt2 miRNA cluster to elucidate its functions during development. Like the Sfmbt2 gene, the Sfmbt2 miRNAs were expressed in the placenta predominantly from the paternal allele. Loss of the paternal allele resulted in severely impaired development of the spongiotrophoblast layer, which usually comprises about half of the fetal placenta. This phenotype was associated with fetal developmental delay or lethality, leading to significant decreases in the number of fetuses and their weights at term. Microarray analysis identified that at least 30 miRNAs in the cluster were actively transcribed in wild-type placentas. Among the predicted targets of these miRNAs, 132 genes were upregulated in the miRNA-deleted placentas. Some of the genes most significantly upregulated, including Gkn2 and Runx1, are known to inhibit cell proliferation by inducing cell cycle arrest or apoptosis. Thus, the Sfmbt2 miRNAs play essential roles in promoting trophoblastic cell proliferation in the placenta, cooperating with the host gene under the same paternal expression control.

2017-02-01 | GSE82054 | GEO

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