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The RNA helicase DDX6 regulation in human skeletal myoblasts [eCLIP-seq]

ABSTRACT: The RNA helicase DDX6 regulation in human skeletal myoblasts [eCLIP-seq]

PROVIDER: PRJNA517602 | ENA |

REPOSITORIES: ENA

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The RNA helicase DDX6 regulation in human skeletal myoblasts [eCLIP-seq]

Project description:Analysis of DDX6 eCLIP in human skeletal myoblasts to identify DDX6 target genes, and binding locations.

2019-10-16 | GSE125809 | GEO

RNA-seq of coding RNA from DDX6 knockout human haploid (HAP1) cells

Project description:We performed a genome-scale screen for suppressors of interferon stimulated gene (ISG) expression in human haploid cells (HAP1). DEAD-box helicase 6 (DDX6) was a significant hit. In order to validate DDX6 as a regulator of ISG expression, we created knockouts of DDX6 in HAP1 cells using CRISPR-Cas9 and performed RNA-seq on coding RNA from DDX6 KO and WT cells. This data was used to determine if ISGs were upregulated in DDX6 KO HAP1 cells.

2017-07-25 | E-MTAB-5867 | biostudies-arrayexpress

Large-scale study of total and polysomial mRNA after DDX6 depletion in HEK293 cells

Project description:DDX6 is an abundant cytoplasmic DEAD-box RNA helicase which is involved in disparate aspects of mRNA stability and translation, leading to a confused understanding of its global function. We carried out a large-scale study of total and polysomial mRNA after DDX6 depletion to get an accurate picture of its roles in human cells.

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Embryonic Skeletal Myoblasts

Project description:Skeletal muscle cells (myoblasts - human fetal cells from 17 week old embryo) Keywords: other

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The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [RNA-seq2]

Project description:Post-transcriptional mechanisms have the potential to influence complex changes in gene expression, yet their role in cell fate transitions remain largely unexplored. Here, we show that the RNA helicase DDX6 is crucial for the dissolution of the pluripotency-specific transcriptional network in mouse and human embryonic stem cells (ESCs). We further demonstrate that epigenetic silencing of DDX6 endows primed ESCs with a differentiation-resistant, “hyper-pluripotent” state, which readily reprograms to a naïve state resembling the preimplantation embryo. In addition to directing cell fate in ESCs, we find that DDX6 plays a key role in adult progenitors where it controls the balance between self-renewal and differentiation in a context-dependent manner. Specifically, DDX6 loss blocks the differentiation of mouse intestinal stem cells and human neural stem cells, while it favors exit from the progenitor state in human muscle and mesenchymal progenitors. Mechanistically, we show that DDX6 coordinates the storage and translational suppression of target mRNAs in P-bodies. Upon loss of DDX6 or mutation of its helicase domain, P-bodies dissolve and release mRNAs encoding fate-instructive transcription and chromatin factors that subsequently re-enter the ribosome pool. Increased translation of these targets impacts cell fate by rewiring the enhancer, heterochromatin and DNA methylation landscapes of human undifferentiated cell types. Collectively, our data establish a novel link between P-body homeostasis, chromatin organization and cellular potency across diverse stem and progenitor cell populations.

2019-10-16 | GSE134164 | GEO

mRNA transcriptome analysis of Ddx6 knockout embryos

Project description:DDX6 is an RNA helicase and involved in various post-transcriptional regulatory processes. Although DDX6 is an evolutionarily well conserved central player in post-transcriptional gene regulation, its function in embryonic development remains obscure. To study this, we examined Ddx6 knockout mouse embryos and pluripotent cell lines. E8.5 Ddx6 mutants exhibited gastrulation defects. To transcriptomically identify the existing cell population in E8.5 mutant embryos and further find the possible causes of this defect, we performed RNA-seq analysis with E8.5 embryo cDNA libraries.

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ChIP-seq of GATA4 in mouse skeletal muscle myoblasts

Project description:GATA4 occupancy on the mouse genome of satellite cell-derived primary myoblasts. Proliferating myoblasts cultured in growth medium were immunoprecipitated with anti-GATA4 antibody or control IgG. Precipitated genomic DNAs were subjected to next generation sequencing. Paired-end 150 bp sequence reads of GATA4-ChIP and IgG-ChIP using mouse skeletal muscle myoblasts.

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Microtranscriptome changes upon Human Skeletal Myoblasts differentiation

Project description:Microtranscriptome changes upon Human Skeletal Myoblasts differentiation

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MEF2C knock-down in Human Skeletal Myoblasts

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