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

ABSTRACT: 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

ORGANISM(S): Mus musculus

PROVIDER: GSE224297 | GEO | 2023/08/07

REPOSITORIES: GEO

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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

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

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.

2020-10-15 | GSE143523 | 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

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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

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

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

Genome-wide Maps of Chromatin State in Control and DEK-deficient Hematopoietic Stem Cells [CUT&Tag]

Project description:Purpose:To identify chromatin state involved in the DEK regulating gene expression of hematopoietic stem cells (HSC) in mice, we performed DEK, H3K27ac, H3K4me3 and H3K9ac CUT&Tag in HSC or LSK cells freshly sorted from mice.

2021-02-22 | GSE166433 | GEO

The FSHD effector protein Dux promotes myopathy via Myostatin-Smad signaling

Project description:Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal-dominant condition that is characterised by a progressive degeneration and weakness of skeletal muscle fibers. The underlying cause of FSHD has been attributed to inappropriate expression of the transcription factor double homeobox (Dux); however, the mechanisms leading to myopathy in response to Dux expression remain incompletely understood. To study the acute effects of Dux activation in mammalian skeletal muscle fibers, we generated a recombinant adeno-associated viral vector allowing tunable Dux expression. Consistent with previous findings, we confirmed that the ectopic expression of Dux in mouse skeletal muscle results in a degenerative myopathy. Building on these findings, we observed that the acute expression of Dux in muscle fibers causes profound transcriptome changes prior to the onset of pathology. Furthermore, muscles expressing Dux display elevated levels of the TGF-beta superfamily member, Myostatin and increased Smad2/3 activity. Notably, inhibition of Myostatin is sufficient to prevent Dux-induced myopathy. Collectively, these findings support further investigation of interventions targeting the Myostatin-Smad2/3 pathway as prospective approaches to treating myopathy associated with Dux mis-expression.

2021-12-31 | GSE108828 | GEO

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