Expression data from Tnrc6a (GW182) mutant E18.5 lungs
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE89327 | GEO | 2017/05/01
SECONDARY ACCESSION(S): PRJNA351798
REPOSITORIES: GEO
Similar Datasets
Project description:GW182 (Tnrc6a) is a key component of RISC (miRNA-Induced Silencing Complex) that plays a critical role in miRNA-mediated gene silencing. Here, we show that GW182 is expressed in the yolk sac endoderm, and that gene-trap disruption of GW182 leads to growth arrest of yolk sac endoderm, impaired hematopoiesis and embryonic lethality. To investigate roles of GW182 in the yolk sac endoderm, we assessed changes in mRNA expression in the yolk sac of E9.5 GW182gt/gt embryos using microarrays (Affymetrix).
2011-09-01 | GSE30244 | GEO
Project description:GW182 (Tnrc6a) is a key component of RISC (miRNA-Induced Silencing Complex) that plays a critical role in miRNA-mediated gene silencing. Here, we show that GW182 is expressed in the yolk sac endoderm, and that gene-trap disruption of GW182 leads to growth arrest of yolk sac endoderm, impaired hematopoiesis and embryonic lethality. To investigate roles of GW182 in the yolk sac endoderm, we assessed changes in mRNA expression in the yolk sac of E9.5 GW182gt/gt embryos using microarrays (Affymetrix). Yolk sac of wild type littermates and GW182gt/gt embryos at E9.5 was collected for total RNA isolation using Trizol (Invitrogen). RNAs were purified according to the manufacturer’s protocol before subjected to Mouse Gene 1.0 ST Whole Genome Array (Affymetrix) for mRNA expression profiling. Experiments were performed in triplicate. Differentially expressed mRNAs were identified using a two-sample t-test (P<0.05 considered significant).
2011-08-31 | E-GEOD-30244 | biostudies-arrayexpress
Project description:microRNAs (miRNAs) regulate a wide variety of biological processes by silencing their target genes. Argonaute (AGO) proteins load miRNAs to form RNA-induced silencing complex (RISC), which mediates translational repression and/or mRNA decay of the targets. A scaffold protein called GW182 directly binds AGO and the CCR4-NOT deadenylase complex, initiating the mRNA decay reaction. Although previous studies have demonstrated the critical role of GW182 in vitro and in cultured cells, its biological significance in living organisms remains largely unexplored. Here, we generated gw182-null flies using the CRISPR/Cas9 system and found that, unexpectedly, they can survive until an early second instar larval stage. Moreover, in vivo miRNA reporters can be effectively repressed even in the absence of GW182. Nevertheless, gw182-null flies have defects in expression of chitin-related genes and formation of the larval trachea system, preventing them to complete the larval development. Our results highlight the importance of both GW182-depedent and -independent silencing mechanisms in vivo.
2024-09-29 | GSE267756 | GEO
Project description:microRNAs (miRNAs) regulate a wide variety of biological processes by silencing their target genes. Argonaute (AGO) proteins load miRNAs to form RNA-induced silencing complex (RISC), which mediates translational repression and/or mRNA decay of the targets. A scaffold protein called GW182 directly binds AGO and the CCR4-NOT deadenylase complex, initiating the mRNA decay reaction. Although previous studies have demonstrated the critical role of GW182 in vitro and in cultured cells, its biological significance in living organisms remains largely unexplored. Here, we generated gw182-null flies using the CRISPR/Cas9 system and found that, unexpectedly, they can survive until an early second instar larval stage. Moreover, in vivo miRNA reporters can be effectively repressed even in the absence of GW182. Nevertheless, gw182-null flies have defects in expression of chitin-related genes and formation of the larval trachea system, preventing them to complete the larval development. Our results highlight the importance of both GW182-depedent and -independent silencing mechanisms in vivo.
2024-09-29 | GSE192811 | GEO
Project description:Here, we dissect the function of GW182 protein in the cnidarian Nematostella, separated by 600 million years from other Metazoa. Using cultured human cells, we show that Nematostella GW182 recruits the CCR4-NOT deadenylation complexes via its tryptophan-containing motifs, thereby inhibiting translation and promoting mRNA decay. Further, similarly to bilaterians, GW182 in Nematostella is recruited to the miRNA repression complex via interaction with Argonaute proteins, and functions downstream to repress mRNA. Thus, our work suggests that this mechanism of miRNA-mediated silencing was already active in the last common ancestor of Cnidaria and Bilateria. Despite this remarkable mechanistic conservation Argonaute and GW182 differentially co-evolved in bilaterians and cnidarians seemingly leading to distinct interaction surfaces.
2016-09-27 | PXD004668 | Pride
Project description:MicroRNAs are small non-coding RNA molecules mediating the translational repression and degradation of target mRNAs in the cell. Mature miRNAs are used as a template by the RNA-induced silencing complex (RISC) to recognize the complementary mRNAs to be regulated. To discern further RISC complex functions, we analyzed the activities of two RISC proteins, AGO2 and GW182, in the MCF-7 human breast cancer cell line. We performed three RIP-Chip experiments using either anti-AGO2 or anti-GW182 antibody and compiled a dataset made up of the miRNA and mRNA expression profiles of three samples for each experiment. Specifically, we analyzed the input sample, the immunoprecipitated fraction and the unbound sample resulting from the RIP experiment. We used the expression profile of the input sample to compute several variables, using formulae capable of integrating the information on predicted miRNA binding sites, both in the 3’UTR and coding regions, with miRNA and mRNA expression level profiles. We compared immunoprecipitated vs unbound samples to determine the differentially expressed genes, independently for AGO2 and GW182 related samples. For each of the two proteins, we trained and tested several support vector machine algorithms able to predict the differentially expressed genes that were experimentally detected. The most efficient algorithm for predicting the over-expressed genes in AGO2 immunoprecipitated samples was trained by using variables involving the number of binding sites in both the 3’UTR and coding region, integrated with the miRNA expression profile, as expected for miRNA targets. On the other hand, we found that the best variable for predicting over-expressed genes in the GW182 immunoprecipitated sample was the length of the coding region. Due to the major role of GW182 in GW/P-bodies, our data suggests that the AGO2-GW182 RISC complex recruits genes based on miRNA binding sites in the 3’UTR and coding region, but only the longer mRNAs remain sequestered in GW/P-bodies, functioning as a repository for translationally silenced RNAs.
2018-09-05 | GSE109666 | GEO
Project description:MicroRNAs are small non-coding RNA molecules mediating the translational repression and degradation of target mRNAs in the cell. Mature miRNAs are used as a template by the RNA-induced silencing complex (RISC) to recognize the complementary mRNAs to be regulated. To discern further RISC complex functions, we analyzed the activities of two RISC proteins, AGO2 and GW182, in the MCF-7 human breast cancer cell line. We performed three RIP-Chip experiments using either anti-AGO2 or anti-GW182 antibody and compiled a dataset made up of the miRNA and mRNA expression profiles of three samples for each experiment. Specifically, we analyzed the input sample, the immunoprecipitated fraction and the unbound sample resulting from the RIP experiment. We used the expression profile of the input sample to compute several variables, using formulae capable of integrating the information on predicted miRNA binding sites, both in the 3’UTR and coding regions, with miRNA and mRNA expression level profiles. We compared immunoprecipitated vs unbound samples to determine the differentially expressed genes, independently for AGO2 and GW182 related samples. For each of the two proteins, we trained and tested several support vector machine algorithms able to predict the differentially expressed genes that were experimentally detected. The most efficient algorithm for predicting the over-expressed genes in AGO2 immunoprecipitated samples was trained by using variables involving the number of binding sites in both the 3’UTR and coding region, integrated with the miRNA expression profile, as expected for miRNA targets. On the other hand, we found that the best variable for predicting over-expressed genes in the GW182 immunoprecipitated sample was the length of the coding region. Due to the major role of GW182 in GW/P-bodies, our data suggests that the AGO2-GW182 RISC complex recruits genes based on miRNA binding sites in the 3’UTR and coding region, but only the longer mRNAs remain sequestered in GW/P-bodies, functioning as a repository for translationally silenced RNAs.
2018-09-05 | GSE109665 | GEO
Project description:Here, we dissect the function of GW182 protein in the cnidarian Nematostella, separated by 600 million years from other Metazoa. Using cultured human cells, we show that Nematostella GW182 recruits the CCR4-NOT deadenylation complexes via its tryptophan-containing motifs, thereby inhibiting translation and promoting mRNA decay. Further, similarly to bilaterians, GW182 in Nematostella is recruited to the miRNA repression complex via interaction with Argonaute proteins, and functions downstream to repress mRNA. Thus, our work suggests that this mechanism of miRNA-mediated silencing was already active in the last common ancestor of Cnidaria and Bilateria. Despite this remarkable mechanistic conservation Argonaute and GW182 differentially co-evolved in bilaterians and cnidarians seemingly leading to distinct interaction surfaces.
2017-03-29 | MSV000080764 | MassIVE
Project description:RNA silencing pathways are conserved gene regulation mechanisms that lead to degradation, translational repression or transcriptional silencing of target-transcripts selected based on complementarity with small RNA molecules. Using firefly luciferase reporters, we previously were able show that the RNA binding protein GW182 plays a role in microRNA-mediated gene silencing (Rehwinkel, J. et al., RNA J. 2005). In this study, we provide further evidence for the role GW182 in the miRNA pathway by determining targets regulated by this protein at the genomic level. We examined expression profiles in Drosophila cells depleted of GW182 and compared these profiles to data obtained from cells depleted of AGO1, a key effector of miRNA-mediated gene silencing.
2006-10-31 | E-MEXP-487 | biostudies-arrayexpress
Project description:RIP-sequencing in mouse embryonic stem cells. Experiment 1 (Samples 1-18): Base cell line (untagged control cells): GFP_5xT71BS (mES [129S6/SvEvTac], yGlob [GFP_5xT71BS], stable transfection FLAG-Cas9::T2A::Blasticidin). HA-Tnrc6a: endogenously HA-AVI-tagged Tnrc6a. HA-Tnrc6a_Trim71KO: HA-AVI-tagged Tnrc6a, Trim71-/-. Experiment 2 (Samples 19-42): Ctrl: base cell line GFP_5xT71BS. Tnrc6a: endogenously HA-AVI-tagged Tnrc6a. Tnrc6a_Trim71KO: HA-AVI-tagged Tnrc6a, Trim71-/-. Tnrc6a_Ago2KO: HA-AVI-tagged Tnrc6a, Ago2-/-.
2023-06-26 | GSE205966 | GEO