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ZSCAN4-binding motif - TGCACAC is conserved and enriched in CA/TG microsatellites in both mouse and human genomes [ChIP-Seq]

ABSTRACT: ZSCAN4-binding motif - TGCACAC is conserved and enriched in CA/TG microsatellites in both mouse and human genomes [ChIP-Seq]

PROVIDER: PRJNA1019288 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26128014.fastq.gz	Fastqsanger.gz
	SRR26128015.fastq.gz	Fastqsanger.gz
	SRR26128016.fastq.gz	Fastqsanger.gz
	SRR26128017.fastq.gz	Fastqsanger.gz
	SRR26128018.fastq.gz	Fastqsanger.gz

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ZSCAN4-binding motif - TGCACAC is conserved and enriched in CA/TG microsatellites in both mouse and human genomes [RNA-Seq]

Project description:The Zinc finger and SCAN domain containing 4 (Zscan4) protein, expressed transiently in pluripotent stem cells as well as in gamete and embryonic development, regulates genome stability in addition to telomere elongation and karyotype correction in mouse ES cells. However, the mechanism underlying Zscan4’s ability to counter the toxic effects of DNA/chromatin remodeling is not fully understood. In this study, we used ChIP-seq technology with Zscan4 antibodies to identify genome-wide binding sites in mouse and human ES cells. We discovered that both mouse and human Zscan4 bind to specific simple sequence repeats, (TG/CA)n, that have a propensity to induce genomic instability through a left-handed helix and stem-loop structure. Furthermore, we found that Zscan4 removes active histone marks from (TG/CA)n regions to maintain the closed/inactive chromatin state. These results demonstrate that Zscan4 protects unstable genomic regions by directing chromatin condensation.

2024-01-25 | GSE243627 | GEO

ZSCAN4-binding motif - TGCACAC is conserved and enriched in CA/TG microsatellites in both mouse and human genomes [ChIP-Seq]

2024-01-25 | GSE243626 | GEO

ZSCAN4-binding motif - TGCACAC is conserved and enriched in CA/TG microsatellites in both mouse and human genomes

Project description:ZSCAN4-binding motif - TGCACAC is conserved and enriched in CA/TG microsatellites in both mouse and human genomes

| PRJNA1019280 | ENA

ZSCAN4-binding motif - TGCACAC is conserved and enriched in CA/TG microsatellites in both mouse and human genomes [RNA-Seq]

Project description:ZSCAN4-binding motif - TGCACAC is conserved and enriched in CA/TG microsatellites in both mouse and human genomes [RNA-Seq]

| PRJNA1019287 | ENA

ZSCAN4-binding motif-TGCACAC is conserved and enriched in CA/TG microsatellites in both mouse and human genomes.

Project description:The Zinc finger and SCAN domain containing 4 (ZSCAN4) protein, expressed transiently in pluripotent stem cells, gametes, and early embryos, extends telomeres, enhances genome stability, and improves karyotypes in mouse embryonic stem (mES) cells. To gain insights into the mechanism of ZSCAN4 function, we identified genome-wide binding sites of endogenous ZSCAN4 protein using ChIP-seq technology in mouse and human ES cells, where the expression of endogenous ZSCAN4 was induced by treating cells with retinoic acids or by overexpressing DUX4. We revealed that both mouse and human ZSCAN4 bind to the TGCACAC motif located in CA/TG microsatellite repeats, which are known to form unstable left-handed duplexes called Z-DNA that can induce double-strand DNA breaks and mutations. These ZSCAN4 binding sites are mostly located in intergenic and intronic regions of the genomes. By generating ZSCAN4 knockout in human ES cells, we showed that ZSCAN4 does not seem to be involved in transcriptional regulation. We also found that ectopic expression of mouse ZSCAN4 enhances the suppression of chromatin at ZSCAN4-binding sites. These results together suggest that some of the ZSCAN4 functions are mediated by binding to the error-prone regions in mouse and human genomes.

| S-EPMC10785592 | biostudies-literature

ZSCAN4-binding motif - TGCACAC is conserved and enriched in CA/TG microsatellites in both mouse and human genomes

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

2024-01-25 | GSE243628 | GEO

CHIP-seq analysis about Histones and Zscan4 after Zscan4 overexpression

Project description:Transcription factor Zscan4 was newly discovered to be a marker of the intermediate state of 2-cell like cells . In addition, the WGCNA discovered a strong positive correlation between the expression of Zscan4 and that of MT2/MERVL .Hence, we examined the possibility for Zscan4 as an activator of MT2/MERVL.

2019-07-08 | GSE125238 | GEO

Microsatellites for Cryptocarya mandioccana

Project description:Microsatellites for Cryptocarya mandioccana

| PRJEB22694 | ENA

Rejuvenation of pluripotent stem cells by frequent activation of Zscan4, Part B

Project description:The gold standard for examining pluripotency of stem cells is to see whether cells can contribute to entire body of animals. Here we show that the increased frequency of Zscan4 activation in mouse ES cells not only enhances, but also maintains their developmental potency in long-term cell culture. As the potency increases, even a whole animal can be produced from a single ES cell injected into 4N blastocyst at unusually high success rate. Although Zscan4-activated cells express genes that are also expressed in 2-cell stage mouse embryos, transiently Zscan4-activated state of ES cells is not associated with the high potency of ES cells. It is thus concluded that ES cells acquire higher potency by going through transient Zscan4 activation state more frequently than the regular state. Taken together, our results indicate that frequent activation of Zscan4 can rejuvenate pluripotent stem cells. Previously, we have shown that constitutive and strong expression of Zscan4 arrest the proliferation of ES cells (refs). We sought for the system to mimic the transient expression of Zscan4 and decided to use ERT2 - Tamoxifen-inducible system (refs). The system allows one to keep a transgene off in the absence of Tmx and turn on in the presence of Tmx at will (refs). We first made a plasmid construct pCAG-Zscan4-ERT2, in which ZSCAN4 ORF fused with ERT2 domain can be driven by a strong ubiquitous promoter CAG. To further investigate this, we transfected pCAG-Zscan4-ERT2 plasmid into an F1 hybrid (C57BL/6J vs. 129) ES cell line V6.5 and isolated multiple cell clones. Based on the qRT-PCR analysis of Zscan4 ORF, we found that cell clones showed a variety of Zscan4 expression levels. We selected the clone that showed the highest Zscan4 expression levels (clone #18) and a clone #2 with the background Zscan4 level.

2013-06-12 | E-GEOD-26162 | biostudies-arrayexpress

CHIP-seq analysis about Histones and Zscan4 after Zscan4 overexpression

Project description:CHIP-seq analysis about Histones and Zscan4 after Zscan4 overexpression

| PRJNA515624 | ENA