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RNA-sequencing in mESCs with overexpression of mCherry-tagged DUX and DUX domain derivatives

ABSTRACT: RNA-sequencing in mESCs with overexpression of mCherry-tagged DUX and DUX domain derivatives

PROVIDER: PRJNA930479 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23310517_1.fastq.gz	Fastqsanger.gz
	SRR23310517_2.fastq.gz	Fastqsanger.gz
	SRR23310518_1.fastq.gz	Fastqsanger.gz
	SRR23310518_2.fastq.gz	Fastqsanger.gz
	SRR23310519_1.fastq.gz	Fastqsanger.gz

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RNA-sequencing in mESCs with overexpression of mCherry-tagged DUX and DUX domain derivatives

Project description:To investigate the requirement of DUX domains for target gene expression, we created clonal stable cell lines in Dux-/- mouse embryonic stem cells and expressed constructs for 12 hours with 0.25 ug/mL doxycycline We then performed gene expression profiling analysis using data obtained from RNA-seq of 11 different cell lines at one time point

2023-08-07 | GSE224296 | GEO

CUT&Tag for DUX recruitment,domain-influenced chormatin modifications, and a potential binding partner with a member of the SWI/SNF complex

Project description:In order to determine that CUT&Tag is similar to known DUX ChIP-seq, we performed CUT&Tag with a mCherry-tagged DUX (with the mCherry antibody). Once confirmed, we pewrformed CUT&Tag for other DUX derivatives with their mCherry tag Then, we performed CUT&Tag for H3K9ac, which is known to globally increase in 2-cell-like cells, which occurs after DUX expression, and CUT&Tag for SMARCC1, a subunit of the SWI/SNF complex

2023-08-07 | GSE224297 | 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

Dux cluster duplication ensures full activation of totipotent genes

Project description:Zygotic genome activation (ZGA) confers to the mouse two-cell (2C)embryo a unique transcriptional profile characterized by transient up-regulation of many totipotency-related genes and MERVL retrotransposons. Intriguingly, those genes are duplicated and clustered in the genome during evolution, including Dux cluster, Obox and Zscan4 family members in mice. However, the contribution and biological significance of the totipotency-related gene duplication events in early embryo development remain poorly understood. Here, we focus on Dux cluster, the master regulator of ZGA that is necessary and sufficient for the induction of 2C-like cells (2CLCs) and activation of totipotency-related genes in mouse embryonic stem cells (mESCs). By reducing Dux gene copies from 31 to 0 or 1 through CRISPR-Cas9 technology, we generate Dux-KO and Dux (n=1)mESC lines, respectively. We uncover that the totipotency-related gene transcriptional profile is awakened to a much lesser extent in Dux (n=1) mESCs compared to wild-type (WT) mESCs following global DNA demethylation reprogramming or induction of DNA damage, mimicking the intrinsic events in preimplantation development. Together, Dux cluster duplication is critically required for the full activation of ZGA transcripts.

2025-02-18 | GSE280037 | GEO

DUX

Project description:DUX

| PRJNA930481 | ENA

A TRIM66/DAX1/Dux axis suppresses the totipotent 2-cell-like state in murine embryonic stem cells

Project description:2 cell-like cells (2CLCs) resemble blastomeres of the 2-cell stage of embryo and are used as an in vitro model to understand the onset of zygotic genome activation (ZGA). 2CLCs comprise only ~1% of murine embryonic stem cells (mESCs). However, their specification remains unclear. Here, we show that TRIM66 restricts 2CLCs specification by repressing Dux in mESCs. Mutational assays and a solved crystal structure demonstrate that TRIM66’s PHD finger recognizes H3K4K9me3 and Bromo domain recognizes H3K18ac. Moreover, TRIM66 functions as a bridge factor to recruit the transcriptional repressor Dax1 to the Dux promoter preventing expansion of 2CLCs in mESCs. Rrecruitment of Dax1 to the Dux promoter requires TRIM66 and TRIM66’s repressive effect on Dux transcription is dependent on Dax1. Thus, beyond expanding the scope of known regulators of 2CLCs and showing TRIM66 as a chromatin-modification reader, our study suggests multiple strategies for harnessing the biotechnological and medical potential of 2CLCs.

2022-06-02 | GSE169450 | GEO

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

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

2015-12-11 | GSE75791 | GEO

The organoid generated from murine small intestine: mCherry-positive vs. mCherry-negative

Project description:The organoids heterogenously expressed mCherry by the lentivirus transduction were dissociated into single cells. A single mCherry- positive and -negative cell were collected and grown up to the organoids, respectivery. The difference of the gene expression profile between mCherry- positive and -negative organoids was assessd by maicroarray.

2014-07-16 | GSE59425 | GEO

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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