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MRNA expression analysis of undifferentiated Dicer +/- (D4) and Dicer -/- (27H10) embryonic cell lines

ABSTRACT: We have analyzed the transcript expression levels in Dicer heterozygous and Dicer knock-out embryonic stem (ES) cells in order to identify which transcripts are regulated by RNAi pathway in mouse ES cells. Keywords: Cell type comparison of cell line with or without knock-out

ORGANISM(S): Mus musculus

PROVIDER: GSE7141 | GEO | 2008/01/01

SECONDARY ACCESSION(S): PRJNA98179

REPOSITORIES: GEO

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Transcription profiling of mouse undifferentiated Dicer +/- (D4) and Dicer -/- (27H10) embryonic cell lines

Project description:We have analyzed the transcript expression levels in Dicer heterozygous and Dicer knock-out embryonic stem (ES) cells in order to identify which transcripts are regulated by RNAi pathway in mouse ES cells. Experiment Overall Design: Two cell lines were analysed in an undifferentiated state. Triplicates of both cell lines were analyzed.

2008-06-15 | E-GEOD-7141 | biostudies-arrayexpress

mRNA expression analysis of undifferentiated Dicer -/- (27H10) embryonic stem cells after miRNA transfection

Project description:We have analyzed the transcript expression levels in Dicer knock-out embryonic stem (ES) cells 24 hours after transfection with either control siRNA agains Renilla luciferase or miRNA Mimics (Dharmacon) of mmu-miR-290 cluster members in order to identify primary targets of miR-290 cluster miRNAs. Keywords: Comparison of effect of two different transfections on transcriptome of Dicer-KO ES cells

2008-01-01 | GSE8503 | GEO

siRNA of mouse undifferentiated Dicer -/- (27H10) embryonic stem cells

Project description:We have analyzed the transcript expression levels in Dicer knock-out embryonic stem (ES) cells 24 hours after transfection with either control siRNA agains Renilla luciferase or miRNA Mimics (Dharmacon) of mmu-miR-290 cluster members in order to identify primary targets of miR-290 cluster miRNAs. Experiment Overall Design: Cell were analysed 24h after transfections in an undifferentiated state. Triplicates of both transfections were analyzed.

2008-06-16 | E-GEOD-8503 | biostudies-arrayexpress

Short RNA profiling of ES cells with and without Dicer

Project description:To better understand Dicer function, and the potential mechanisms by which RNAi contributes to pluripotency, short RNA expression was profiled from 4 ES cell libraries: 2 made from a Dicer-conditional ES cell line before and several months after deletion of Dicer, and 2 made before and 5 days after demethylation of J1 ES cells with 5-aza-deoxycytidine. Contributed here are the unannotated sequence data from each library, including those sequences that did not match the mouse genome or any known non-coding RNAs. Keywords: 454 sequencing, miRNA, dicer, demethylation

2007-10-31 | GSE9306 | GEO

Dicer conditional knockout embryonic heart mutant vs control array

Project description:The goal is to find out the gene expression changes when Dicer was inactivated in the murine heart. Keywords: Dicer mutant Dicer gene was specifically inactivated in the mouse heart using cardiac specific Nkx2.5 Cre knock-in line. Embryonic day 11.5 heart from mutant and control hearts were compared in triplicates.

2010-06-11 | E-GEOD-7343 | biostudies-arrayexpress

The RIG-I like receptor LGP2 inhibits Dicer-dependent processing of long double-stranded RNA and blocks RNA interference in mammalian cells.

Project description:In vertebrates, the presence of viral RNA in the cytosol is sensed by members of the RIG-I like receptor (RLR) family , which signal to induce production of type I interferons (IFN). These key anti-viral cytokines act in a paracrine and autocrine manner to induce hundreds of interferon-stimulated genes (ISGs), whose protein products restrict viral entry, replication and budding. ISGs include the RLRs themselves: RIG-I, MDA5 and the least-studied family member, LGP2. In contrast, the IFN system is absent in plants and invertebrates, which defend themselves from viral intruders using RNA interference (RNAi). In RNAi, the endoribonuclease Dicer cleaves virus-derived double stranded RNA (dsRNA) into small interfering RNAs (siRNAs) that target complementary viral RNA for cleavage. Interestingly, the RNAi machinery is conserved in mammals and we have recently demonstrated that it is able to participate in mammalian antiviral defence in conditions in which the IFN system is suppressed. In contrast, when the IFN system is active, one or more ISGs act to mask or suppress antiviral RNAi. Here, we demonstrate that LGP2 constitutes one of the ISGs that can inhibit antiviral RNAi in mammals. We identify Dicer as an LGP2-associated protein and show that LGP2 inhibits Dicer cleavage of dsRNA into siRNAs both in vitro and in vivo. Further, we show that in cells lacking an IFN response, ectopic expression of LGP2 interferes with RNAi-dependent suppression of gene expression. Thus, the inefficiency of RNAi as a mechanism of antiviral defence in mammalian somatic cells can be in part attributed to Dicer inhibition by LGP2 induced by type I IFNs.

2018-01-17 | PXD008364 | Pride

Expression data from NcGFP ki/+, NcGFP ki/ki and wt (W4) ES cells

Project description:We generated a gene replacement allele of the E-cadherin locus that express an N-cadherin-GFP fusion in ES cells. Expression profiles of homozygous and heterozygous knock-in ES cells were analyzed in comparison to wt ES cells. The GEO Samples were compared to published data of E-cadherin knock-out ES cells (ArrayExpress, accession number E-MEXP-2836). The comparison data are linked below.

2013-07-01 | GSE42008 | GEO

Phosphoproteomic analysis of liver of Dicer knockout mice

Project description:Dicer is an essential ribonuclease involved in the biogenesis of miRNA. Previous studies have reported that Dicer is dysregulated in multiple types of cancers. To investigate the downstream phosphoproteome of Dicer, we carried out phosphotyrosine profiling of the liver of Dicer knockout of mice. We employed antibody-based enrichment of phosphotyrosine containing peptides coupled with spike-in SILAC-based quantitation. Over 400 phosphoisites were identified in each condition while 290 phosphosites were quantitated in common. Amongst these, several key signaling molecules like receptor tyrosine kinase MET, MET, PDGFR, EPHA2, EPHB4 and IGF1R/INSR were hyperphosphorylated. Also, non-receptor tyrosine kinases of Src family and their downstream effector signaling partners including IRS2 and STAT3were found to be hyperphosphorylated. Our study indicates that there is significant alteration in the signaling pathways upon ablation of Dicer.

2016-07-08 | PXD000927 | Pride

A retrotransposon-driven Dicer variant enhances endogenous RNAi in mouse oocytes

Project description:Mammals have one Dicer gene required for biogenesis of small RNAs in microRNA (miRNA) and RNA interference (RNAi) pathways. Yet, endogenous RNAi is highly active in oocytes but not in somatic cells. Here, we provide a mechanistical explanation for high RNAi activity in mouse oocytes. The main Dicer isoform in oocytes is transcribed from an intronic MT-C retrotransposon, which functions as a promoter of an oocyte-specific Dicer isoform (denoted DicerO). DicerO lacks an N-terminal helicase domain and has a higher cleavage activity than the full-length Dicer from somatic cells. DicerO can rescue the miRNA pathway and, in addition, it efficiently produces small RNAs from long dsRNA substrates. Thus, control of endogenous RNAi activity in mice occurs via alternative Dicer isoform and the phylogenetic origin of DicerO demonstrates evolutionary plasticity of RNA silencing pathways.

2013-11-07 | GSE41207 | GEO

An isoform of Dicer protects mammalian stem cells against multiple RNA viruses

Project description:In mammals, early resistance to viruses relies on interferons, which protect differentiated but not stem cells from viral replication. Many other organisms rely instead on RNA interference (RNAi) mediated by a specialised Dicer protein that cleaves viral double stranded RNA. Whether RNAi also contributes to mammalian antiviral immunity remains controversial. Here we identify an isoform of Dicer, named antiviral Dicer (aviD), that protects tissue stem cells from RNA viruses, including Zika virus and SARS-CoV-2, by dicing viral double-stranded RNA to orchestrate antiviral RNAi. Our work sheds light on the molecular regulation of antiviral RNAi in mammalian innate immunity in which different cell-intrinsic antiviral pathways are tailored to the differentiation status of cells.

2021-07-09 | GSE173946 | GEO

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