Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Analysis of the genome-wide distribution of RNA Pol II in a neuroblastoma cell line under silencing of RNA helicases DDX5 and DDX17

ABSTRACT: DEAD-box RNA helicases DDX5 and DDX17 regulate gene expression at different levels such as transcription and splicing, but the underlying mechanisms are not fully understood. A calibrated ChIP-seq analysis of total RNA Polymerase II was carried out in DDX5/DDX17-depleted SH-SY5Y cells to analyse the contribution of DDX5/DDX17 to RNAPII distribution. Univ Lyon, ENS de Lyon, CNRS UMR 5239, INSERM U1293, Laboratory of Biology and Modelling of the Cell, 46 Allée d'Italie, F-69007, Lyon, France. Corresponding author: cyril.bourgeois@inserm.fr

ORGANISM(S): Homo sapiens

PROVIDER: GSE183517 | GEO | 2022/08/04

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Analysis of a neuroblastoma cell line transcriptome by polyA+ RNA sequencing under silencing of RNA helicases DDX5 and DDX17

Project description:DEAD-box RNA helicases DDX5 and DDX17 regulate gene expression at different levels such as transcription and splicing, but the underlying mechanisms are not fully understood. A transcriptome analysis of DDX5/DDX17-depleted human cells confirmed was carried out to further characterize the widespread deregulation of alternative splicing. This study also revealed a deregulation of 3’ end processing leading to transcriptional read-through. Univ Lyon, ENS de Lyon, CNRS UMR 5239, INSERM U1293, Laboratory of Biology and Modelling of the Cell, 46 Allée d'Italie, F-69007, Lyon, France. Corresponding author: cyril.bourgeois@inserm.fr

2022-08-04 | GSE183205 | GEO

RNA helicases DDX5 and DDX17 dynamically orchestrate transcription, microRNA and splicing programs in cell differentiation

Project description:RNA helicases DDX5 and DDX17 are members of a large family of highly conserved proteins involved in gene expression regulation, although their in vivo targets and activities in biological processes like cell differentiation, that requires reprogramming of gene expression programs at multiple levels, are not well characterized. In this report, we uncovered a new mechanism by which DDX5 and DDX17 cooperate with hnRNP H/F splicing factors to define epithelial- and myoblast-specific splicing subprograms. We next observed that downregulation of DDX5 and DDX17 protein expression during epithelial to mesenchymal transdifferentiation and during myogenesis contributes to switching splicing programs during these processes. Remarkably, this downregulation is mediated by the production of microRNAs induced upon differentiation in a DDX5/DDX17-dependent manner. Since DDX5 and DDX17 also function as coregulators of master transcriptional regulators of differentiation, we propose to name these proteins M-bM-^@M-^\master orchestratorsM-bM-^@M-^] of differentiation, that dynamically orchestrate several layers of gene expression. 6 samples of MCF7 cells exposed to different treatments were analyzed: 3 x siCTRLM-BM- ; 3 x si(DDX5-17) AND 6 samples of MCF10 cells exposed to different treatments were analyzed: 3 x siCTRLM-BM- ; 3 x si(DDX5-17)

2014-05-06 | E-GEOD-57281 | biostudies-arrayexpress

RNA helicases DDX5 and DDX17 dynamically orchestrate transcription, microRNA and splicing programs in cell differentiation

Project description:RNA helicases DDX5 and DDX17 are members of a large family of highly conserved proteins involved in gene expression regulation, although their in vivo targets and activities in biological processes like cell differentiation, that requires reprogramming of gene expression programs at multiple levels, are not well characterized. In this report, we uncovered a new mechanism by which DDX5 and DDX17 cooperate with hnRNP H/F splicing factors to define epithelial- and myoblast-specific splicing subprograms. We next observed that downregulation of DDX5 and DDX17 protein expression during epithelial to mesenchymal transdifferentiation and during myogenesis contributes to switching splicing programs during these processes. Remarkably, this downregulation is mediated by the production of microRNAs induced upon differentiation in a DDX5/DDX17-dependent manner. Since DDX5 and DDX17 also function as coregulators of master transcriptional regulators of differentiation, we propose to name these proteins “master orchestrators” of differentiation, that dynamically orchestrate several layers of gene expression.

2014-05-06 | GSE57281 | GEO

downregulation of DDX5 and DDX17

Project description:RNAseq : MCF-7 cells were transfected with siRNA targeting both DDX5 and DDX17 RNA helicases, and total RNA were extracted as described previously (Dardenne Cell Rep 2014).

2017-02-02 | GSE94372 | GEO

Downregulation of DDX5/DDX17 and REST

Project description:We aimed at analysing the effect of RNA helicases DDX5 and DDX17 and of the transcription factor REST on gene expression in the human SH-SY5Y neuroblastoma cell line (European Collection of Cell Cultures, ECACC), which was cultured as recommended by the supplier.

2017-12-31 | GSE98871 | GEO

Effect of DDX5/DDX17 on genome-wide RNA Polymerase II distribution in SH-SY5Y cells

Project description:This project includes ChIP of total RNA pol II in human SH-SY5Y neuroblastoma cells following the joint depletion of RNA helicases DDX5 and DDX17 to determine the genome-wide effect of DDX5/DDX17 on RNA Pol II distribution.

2022-09-21 | GSE157850 | GEO

Identification of DDX5 and DDX17 target genes in human ECCs and their neural derivartives

Project description:Neural cell fate specification is a highly regulated process in which stem cells sequentially possess the transcriptional profile changed and give raise to particular cell lineages such as neuron and glial cells. The NTERA2 cell line is one of the well-characterized hEC cells that can be used as a model system for identifying the regulatory network during human pluripotent stem cells differentiated toward the neural lineage. It has been demonstrated that DDX5 and DDX17, as transcriptional co-regulator, can play a role in various cellular mechanisms depending on their interaction with the different types of transcription factors. Here, we performed ChIP-seq for DDX5 and DDX17 to identify their preferential binding targets during stage transition from pluripotent to neural cell lineage.

2022-01-10 | GSE174051 | GEO

Regulation of gene expression in human ECCs and their neural derivatives by DDX5 and DDX17

Project description:The fate of NSCs is strictly controlled by dynamic programs related to time. This process requires an interconnection between intrinsic and extrinsic factors to modulate the gene expression programs and precisely control the action of various downstream signaling. Several studies have been identified the uncovered functions of DDX5 and DDX17 involved in multiple aspects of gene regulatory networks and some of those have been suggested their potential roles regarding neural differentiation. In this study, we sought to distinguish the mode of action of DDX5 and DDX17 underlying the neurogenesis between two distinct cell stages including pluripotent and neural stem cell pools. We employ the ability of RNA interference to investigate the functional involvement of these two RNA helicases during embryonic and adult neurogenesis.

2022-01-10 | GSE173292 | GEO

The RNA helicases DDX5 and DDX17 facilitate neural differentiation of human pluripotent stem cells NTERA2

Project description:The RNA helicases DDX5 and DDX17 facilitate neural differentiation of human pluripotent stem cells NTERA2

| PRJNA728079 | ENA

Splicing switch of an epigenetic regulator by RNA helicases promotes tumor-cell invasiveness

Project description:Both epigenetic and splicing regulation contribute to tumor progression, but the potential links between these two levels of gene-expression regulation in pathogenesis are not well understood. Here, we report that the mouse and human RNA helicases ddx17 and ddx5 contribute to tumor-cell invasiveness by regulating alternative splicing of several DNA- and chromatin-binding factors, including the macroH2A1 histone. We show that macroH2A1 splicing isoforms differentially regulate the transcription of a set of genes involved in redox metabolism. In particular, the SOD3 gene that encodes the extracellular superoxide dismutase and plays a part in cell migration is regulated in an inverse manner by macroH2A1 splicing isoforms. These findings reveal a new regulatory pathway in which splicing factors control the expression of histone-variant isoforms that in turn drive a transcription program to switch tumor cells to an invasive phenotype. We analyzed 4T1 cells depleted or not for ddx5 and ddx17 RNA helicases using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool. Four techinical replicates were performed. We analyzed 4T1 cells depleted for ddx5 and ddx17 RNA helicases and macroH2A1.1 or macroH2A1.2 using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool. Three techinical replicates were performed.

2012-09-11 | E-GEOD-40737 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data