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

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

PROVIDER: PRJNA728075 | ENA |

REPOSITORIES: ENA

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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.

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Identification of DDX5 target genes in spermatogonia

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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.

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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

Identification of DDX5 target genes in spermatogonia

Project description:Sustained spermatogenesis in adult males and recovery of fertility following germ cell depletion are dependent on undifferentiated spermatogonia with self-renewal potential. Self-renewal of undifferentiated spermatogonia is dependent on a complex network of transcriptional and post-transcriptional regulatory factors. DDX5 is known to act as a transcriptional co-regulator in other systems through interactions with key transcription factors. Here, we performed ChIP-Seq to identify target genes of DDX5 in cultured undifferentiated spermatogonia in order to elucidate its role in maintenance of the male germline.

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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

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

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downregulation of DDX5 and DDX17

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

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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.

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