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RNAseq of DUX KO mouse 2-cell embryos

ABSTRACT: RNAseq of DUX KO mouse 2-cell embryos

PROVIDER: PRJNA593050 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10575067_1.fastq.gz	Fastqsanger.gz
	SRR10575067_2.fastq.gz	Fastqsanger.gz
	SRR10575068_1.fastq.gz	Fastqsanger.gz
	SRR10575068_2.fastq.gz	Fastqsanger.gz
	SRR10575069_1.fastq.gz	Fastqsanger.gz

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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

RNAseq of Wildtype, Smchd1 KO, Dux KO, Double KO, Tet-TKO and quadurple KO ES cells

Project description:RNAseq was performed by to compare gene expression between wildtype and Smchd1 KO ES cells, the gene expression pattern in Dux KO mutants , Double KO mutant Tet-TKO mutants and Tet TKO plus SMCKHD1 KO mutants were analyzed by RNAseq.

2021-01-27 | GSE126467 | 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

Loss of DUX causes minor defects in zygotic genome activation and is compatible with mouse development

Project description:How maternal factors in oocytes trigger zygotic genome activation (ZGA) is a long-standing question in developmental biology. Recent studies in 2-cell like embryonic stem cells (2C-like cells) implicate that the DUX family transcription factors are key regulators of ZGA in placental mammals. To characterize the role of DUX in ZGA, we generated Dux cluster knockout (KO) mouse lines. Unexpectedly, we found both Dux zygotic KO (Z-KO) and maternal/zygotic KO (MZ-KO) embryos can survive to adulthood despite showing reduced developmental potential. Furthermore, transcriptome profiling of the MZ-KO embryos revealed that loss of DUX has minimal effect on ZGA and most DUX targets in 2C-like cells are normally activated in MZ-KO embryos. Thus, contrary to the key function in inducing 2C-like cells, our data indicate that DUX only has a minor role in ZGA and loss of DUX is compatible with mouse development.

2019-04-10 | GSE121746 | GEO

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Project description:RNAseq of Wildtype, Smchd1 KO, Dux KO, Double KO, Tet-TKO and quadurple KO ES cells

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Spen regulates X chromosome inactivation (RNAseq in SPEN KO embryos)

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

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

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Parallel analysis of H3K9ac reveals Dux-dependent 2C activation deficiency in mouse SCNT embryos

Project description:Somatic cell nuclear transfer (SCNT) enables gaining of totipotency by reprogramming nuclei of terminally differentiated donor cell. Recent studies have clearly demonstrated that intervention of epigenetic networks can significantly elevate both in vitro and in vivo development potential of NT embryos. Specifically, trichostatin A (TSA), a kind of histone deacetylase inhibitors (HDACi), was proved to functionally works during cloning in various mammal systems. However, how it modulates histone acylation lacks careful illustration. Here, we systematically evaluate the effect and limitation of TSA during SCNT embryo development by generating genome-wide H3K9ac maps. In addition, a Dux-dependent 2-cell (2C) activation deficiency is observed in SCNT embryos as compared with their natural fertilized counterparts. Strikingly, a refined Dux supplement can successfully assist SCNT embryos in overcoming the 2C activation defect and further promotes the overall cloning efficiency. Together, our study for the first time reveals the regulation mechanism of histone marker H3K9ac in SCNT and provides the new insight of Dux during embryogenesis.

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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

The disruption of CtBP regulates DUX-dependent and -independent genetic program for the 2-cell-like state in murine embryonic stem cells [RNA-seq and RRBS]

Project description:After fertilization, maternally deposited mRNA is cleared, and de novo mRNA is transcribed from the zygotic genome through zygotic genome activation (ZGA), which is called maternal-to-zygotic transition (MZT) occurring in the mouse at 2-cell (2C) stage. 2C-like cells (2CLCs) marked by MERVL expression and transcriptionally similar to 2C embryos spontaneously emerge from mouse embryonic stem cells (mESCs). Although the emergence of 2CLCs completely depends on DUX function, a recent knockout study clearly showed that DUX is dispensable for mouse embryos, suggesting that DUX-independent molecular pathways are not recapitulated in 2CLCs. We present here that the disruption of C-terminal binding protein 1/2 (Ctbp1/2) activates DUX-dependent and -independent molecular pathway associated with the development of early mouse embryos mediated by the upregulation of Preferentially expressed antigen of melanoma family-like 7 (PRAMEL7). Furthermore, the abnormality of the gene expression profile caused by Dux KO is partially rescued by the overexpression of PRAMEL7 in mESCs. Our study provides new insights into the DUX-independent molecular pathway for developing early mouse embryos.

2024-05-27 | GSE253944 | GEO

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