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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE57281 | GEO | 2014/05/06

SECONDARY ACCESSION(S): PRJNA246163

REPOSITORIES: GEO

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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

Analysis of the genome-wide distribution of RNA Pol II in a neuroblastoma cell line 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 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

2022-08-04 | GSE183517 | GEO

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

Helicases DDX5 and DDX17 promote Hepatitis B Virus transcription termination heterogeneity in infected human hepatocytes

Project description:Background & Aims: Transcription termination fine tunes gene expression and contributes to specify the function of RNAs in eukaryotic cells. Transcription termination of hepatitis B virus (HBV) is subjected to the recognition of the canonical polyadenylation signal (cPAS) common to all viral transcripts. The regulation of the usage of this cPAS and its impact on viral gene expression and replication is currently unknown. Approach & Results: To unravel the regulation of HBV transcript termination, we used a 3’ RACE-PCR assay together with single molecule sequencing both in in vitro infected hepatocytes and in chronically infected patients. The detection of a previously unidentified transcriptional readthrough indicated that the cPAS was not systematically recognized during HBV replication in vitro and in vivo. After gene expression downregulation, followed by RNA and chromatin immunoprecipitation experiments, we showed the role of the RNA helicases DDX5 and DDX17 in promoting viral transcriptional readthrough, which was, furthermore, associated to HBV RNA destabilization. Moreover, downregulation of DDX5 and DDX17 allowed the precise termination of HBV transcripts at cPAS, which was associated with increased viral replication. Conclusions: Our findings identify DDX5 and DDX17 as crucial determinants for HBV transcriptional fidelity and as host restriction factors for HBV replication.

2024-07-28 | GSE239571 | GEO

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

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

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

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

Homo sapiens

Project description:downregulation of DDX5 and DDX17

| PRJNA369520 | ENA

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

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