Effect of DDX5/DDX17 on genome-wide RNA Polymerase II distribution in SH-SY5Y cells
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE157850 | GEO | 2022/09/21
REPOSITORIES: GEO
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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
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
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
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
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
Project description:THOC5, a member of the THO complex, is essential for the 3´processing of some inducible genes, the export of a subset of genes and stem cell self-renewal. Utilising nanopore mRNA-sequencing we show that when THOC5 is depleted 50% of mRNAs undergo altered 3´end cleavage. Further, THOC5 depletion leads to increased RNA Polymerase II (Pol II) presence on the gene body and close to the 3’end. Moreover, THOC5 is recruited close to high density Pol II sites except those at the promotor regions suggesting that THOC5 is involved in transcriptional elongation. Indeed, THOC5 independent genes in cells expressing fast Pol II became THOC5 dependent in cells expressing slow Pol II. In cells expressing slow Pol II chromatin associated THOC5 interacts with CDK12 (a protein that modulates mRNA elongation rates), RNA helicases DDX5, DDX17, and THOC6. Importantly these interactions were not observed in cells expressing fast Pol II. The CDK12/THOC5 interaction promotes CDK12 recruitment to R-loops in a THOC6-dependent manner. These data demonstrate that THOC5/THOC6 play a part in transcription elongation. Given the role of THOC5 in primitive cell survival its phosphorylation by agonists, oxidative stress and oncogenes the pathway we identified has relevance in the physiology and pathology of stem cells
2022-12-12 | PXD035092 | Pride
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
Project description:THOC5, a member of the THO complex, is essential for the 3´processing of some inducible genes, the export of a subset of genes and stem cell self-renewal. Utilising nanopore mRNA-sequencing we show that when THOC5 is depleted 50-60% of mRNAs undergo altered 3´end cleavage. Further, THOC5 depletion leads to increased RNA Polymerase II (Pol II) presence at the start site, on the gene body and close to the 3’end. Moreover, THOC5 is recruited close to high density Pol II sites suggesting that THOC5 is involved in transcriptional elongation. Indeed, DRB/TTchem-seq that measures elongation rates in vivo revealed an accumulation of released Pol II near to TSS and a decrease of elongation rates in THOC5 depleted cells. Furthermore, THOC5 is more recruited to its target genes in cells expressing slow Pol II than those expressing fast Pol II. In cells expressing slow Pol II chromatin associated THOC5 interacts with CDK12 (a protein that modulates mRNA elongation rates), RNA helicases DDX5, DDX17, and THOC6. Importantly these interactions were not observed in cells expressing fast Pol II. 3’ cleavage of 50% of THOC5 target genes is also regulated by CDK12 and THOC6. The CDK12/THOC5 interaction promotes CDK12 recruitment to R-loops in a THOC6-dependent manner. These data demonstrate that THOC5/THOC6 play a part in transcription elongation. Given the role of THOC5 in primitive cell survival its phosphorylation by agonists, oxidative stress and oncogenes the pathway we identified has relevance in the physiology and pathology of stem cells.
2022-12-16 | GSE173374 | GEO
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
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