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Precise temporal regulation of Dux is important for embryo development

ABSTRACT: Precise temporal regulation of Dux is important for embryo development

PROVIDER: PRJNA556588 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9276060_1.fastq.gz	Fastqsanger.gz
	SRR9276060_2.fastq.gz	Fastqsanger.gz
	SRR9276070_1.fastq.gz	Fastqsanger.gz
	SRR9276070_2.fastq.gz	Fastqsanger.gz
	SRR9276080_1.fastq.gz	Fastqsanger.gz

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Precise temporal regulation of Dux is important for embryo development

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

2019-08-07 | GSE134832 | GEO

Time point RNA-seq of Dux over expression samples reveals different transcriptomes of Dux induction in mESC

Project description:Prevous study has discoverd 2CLC trancriptome and MERVL can be up-regulated by Dux over expression,but rarely has been found about the whole procedure of Dux-induced 2C-entry and exit process and whether this system can reflect the natural 2-cell embryo development,so we we defined different time point transcription after Dux over expression,and try to establish a link between gene expression profile between gene dynamics in different Dux over expression time point and in early mouse embryo development

2023-06-01 | GSE202161 | GEO

DUX

Project description:DUX

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Dux cluster duplication ensures fully activation of totipotent genes

Project description:Mammalian zygotic genome activation (ZGA) following fertilization refers to the process that results in transcriptional awakening of the embryonic genome at two-cell (2C) stage in mice or 4-8 cell stage in human. ZGA confers to the mouse 2C embryo a unique transcriptional profile characterized by transient up-regulation of many totipotency-related genes and MERVL transposons. Intriguingly, many ZGA-related totipotent genes are duplicated and clustered in the genome during evolution, including Dux cluster, OBOX and Zscan4 family members in mice. Yet, the contribution and biological significance of the totipotency-related gene duplication events during evolution in totipotency acquisition remain poorly understood. Here, we focus on Dux cluster, the master regulator of ZGA that is necessary and sufficient for the emergence of 2C-like cells (2CLCs) and activation of target totipotent genes in mouse embryonic stem cells (ESCs). By reducing Dux gene copy number from 31 to 0 or 1 with CRISPR-Cas9 technology, we generated Dux-KO and Dux (n=1) ES cell lines, respectively. We found that the totipotent gene transcriptional profile could not be fully activated in Dux (n=1) mESCs compared to wild type (WT) mESCs after treatment with DNMT1 protein degrader, mimicking the DNA demethylation process during early embryo development. These data demonstrate that Dux cluster duplication is essential for fully activation of totipotency-related genes, ensuring ZGA and totipotency acquisition.

2024-10-12 | GSE263217 | GEO

Assessment of functional overlap between mouse Dux and human DUX4 in vitro and in vivo

Project description:We report both DUX4 and Dux toxicity depend upon their ability to bind DNA and activate transcription. Chromatin immunoprecipitation of V5 epitope tagged human DUX4 and mouse Dux was performed in human myoblasts was analyzed using ChIP-Seq to identify their subsequent binding sites. We found that DUX4 and Dux bind 4-8% of identical sequences, while majority of the binding sites are unique to either DUX4 or Dux. Although small, this overlap could be due to their conserved abilioty to regualte primordial pathways that were essential for life and therefore maintained in both proteins despite their separate evolutionary paths. We performed ChIP-Seq analysis of human myoblasts transfected with plasmids encoding either epitope tagged human DUX4 (1 sample) and mouse Dux (1 sample). Illumina sequencing libraries were prepared from the ChIP and Input DNA, then resulting DNA libraries were quantified and sequenced and aligned to the human genome (hg19).

2015-12-11 | E-GEOD-75791 | biostudies-arrayexpress

Mouse Dux is myotoxic and shares partial functional homology with its human paralog DUX4

Project description:We report the RNA-seq experiments performed in human myoblasts transfected with human DUX4 and mouse Dux. Comparison of genes up- and down-regulated by DUX4 and Dux in human myoblasts to identify pathways similiarly regulated by both transcription factors.

2016-08-24 | E-GEOD-85935 | biostudies-arrayexpress

RNAseq of DUX KO mouse 2-cell embryos

Project description:Some of the earliest transcripts produced in fertilized human and mouse oocytes code for DUX, a double homeodomain protein that promotes embryonic genome activation (EGA). Deleting Dux by genome editing at the 1- to 2-cell stage in the mouse impairs EGA and blastocyst maturation. Here, we demonstrate that mice carrying homozygous Dux deletions display markedly reduced expression of DUX target genes and defects in both pre- and post-implantation development, with notably a disruption of the pace of the first few cell divisions and significant rates of late embryonic mortality. However, some Dux-/- embryos give raise to viable pups, indicating that DUX is important but not strictly essential for embryogenesis.

2019-12-03 | GSE141321 | GEO

Single cell RNA-seq Analysis of Wild Type(WT), Dux knockout(KO) and Dux overexpression(OE) embryos

Project description:We tested the transcriptome of embryos from WT and Dux KO mice including zygotes (hCG 28h), early 2-cell (hCG 31-32h), middle 2-cell(hCG 41-42h), late 2-cell(hCG 47-48h) and, Dux mRNA injected embryos including zygote(5h after injection, hCG 28h), early 4-cell(6h after injection, hCG 54h) and late 4-cell (17h after injection, hCG 65h) using the Covaris DNA shearing protocol for Smart-seq sequence library generation. We found that the activation of Dux is important but not essential for ZGA, but the silencing and elimination of Dux is strictly necessary for early embryonic development.

2019-09-24 | GSE132045 | GEO

DUX domain-dependent chromatin accessibility of DUX binding sites

Project description:To determine whether DUX domain binding to SMARCC1 influence chromatin reodeling at DUX binding sites, we performed ATAC-seq We know DUX binding sites are open at the time of expression, but we do not know which domains are required to be present with the discovery of the C-terminal repeats and 14 amino acid tail

2023-08-07 | GSE224298 | GEO

Spatio-temporal mRNA tracking in the early zebrafish embryo

Project description:Spatio-temporal mRNA tracking in the early zebrafish embryo

| PRJNA666689 | ENA