RNA localization to protrusions of mouse melanoma YUMM1.7 cells.
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE219089 | GEO | 2023/02/24
REPOSITORIES: GEO
Similar Datasets
Project description:Transcriptome analysis of specific mRNA interacting with KIF1C-GFP in HeLa Cells. RNA localization and local translation are involved in a wide range of cellular functions. In mammals, a class of mRNAs localize to cytoplasmic protrusions in an APC dependent manner, with important roles during cell migration. Here, we investigated this localization mechanism. We found that the KIF1C motor interacts with many APC-dependent mRNAs and is required for their localization. Live cell imaging of localizing mRNAs further revealed rapid, active transport of single mRNAs over long distances, and showed that this requires both microtubules and KIF1C. Moreover, two color imaging directly revealed single mRNAs transported by single KIF1C motors, with the 3’UTR of localized mRNAs being sufficient to trigger KIF1C-dependent RNA transport and localization. These results reveal a general RNA transport pathway in mammalian cells, in which the KIF1C motor transports RNAs to cytoplasmic protrusions. Interestingly, KIF1C also transported its own mRNA suggesting a possible feedback loop acting at the level of mRNA transport.
2020-11-13 | GSE161316 | GEO
Project description:3' mRNA-seq of protrusions and cell bodies of nt or LARP6 siRNA transfected MDA-MB231 cells. These data show that Ribosomal protein (RP) -mRNAs localization to cell protrusions is mediated by LARP6.
2022-10-03 | E-MTAB-8472 | biostudies-arrayexpress
Project description:3' mRNA-seq of protrusions and cell bodies of a panel of normal and malignant cell lines. These data show that Ribosomal protein (RP) -mRNAs localization to cell protrusions is a conserved phenomenon.
2020-10-30 | E-MTAB-8470 | biostudies-arrayexpress
Project description:The kinesin KIF1C transports APC-dependent mRNAs to cell protrusions
| PRJNA677869 | ENA
Project description:Deciphering the complex biology of cell migration is key to understand human-related disorders. During angiogenesis, endothelial cells engage in coordinated migration events to form new blood vessels from parental counterparts. However, while subcellular localisation of mRNAs and localised translation are fundamental steps between gene transcription and protein activity, whether local regulation of gene expression controls the complex morphogenetic process of angiogenesis has never been addressed. Here, we set out to investigate the cytoplasmic distribution of mRNAs in migratory endothelial cells. We isolated RNA from endothelial cell protrusions from their cell bodies and used RNA-sequencing to identify asymmetrically distributed transcripts. These studies identified a set of transcripts enriched in endothelial cell protrusions over cell bodies, which included classically protrusion-enriched mRNAs and other intriguing transcripts encoding proteins implicated in cell migration.
2020-09-07 | GSE133055 | GEO
Project description:mRNA trafficking and local protein translation are associated with protrusive cellular domains, such as neuronal growth cones, and deregulated control of protein translation is associated with tumor malignancy. We show here that activated RhoA, but not Rac1, is enriched in pseudopodia of MSV-MDCK-INV tumor cells and that Rho, Rho kinase (ROCK) and myosin II regulate the microtubule-independent targeting of RNA to these tumor cell domains. ROCK inhibition does not affect pseudopodial actin turnover but significantly reduces the dynamics of pseudopodial RNA turnover. Gene array analysis shows that 7.3% of the total genes analyzed exhibited a greater than 1.6-fold difference between the pseudopod and cell body fractions. Of these, only 13.2% (261 genes) are enriched in pseudopodia, suggesting that only a limited number of total cellular mRNAs are enriched in tumor cell protrusions. Comparison of the tumor pseudopod mRNA cohort and a cohort of mRNAs enriched in neuronal processes identified tumor pseudopod-specific signaling networks that were defined by expression of M-Ras and the Shp2 protein phosphatase. Pseudopod expression of M-Ras and Shp2 mRNA were diminished by ROCK inhibition linking pseudopodial Rho/ROCK activation to the localized expression of specific mRNAs. Pseudopodial enrichment for mRNAs involved in protein translation and signaling suggests that local mRNA translation regulates pseudopodial expression of less stable signaling molecules as well as the cellular machinery to translate these mRNAs. mRNA trafficking and local protein translation are associated with protrusive cellular domains, such as neuronal growth cones, and deregulated control of protein translation is associated with tumor malignancy. We show here that activated RhoA, but not Rac1, is enriched in pseudopodia of MSV-MDCK-INV tumor cells and that Rho, Rho kinase (ROCK) and myosin II regulate the microtubule-independent targeting of RNA to these tumor cell domains. ROCK inhibition does not affect pseudopodial actin turnover but significantly reduces the dynamics of pseudopodial RNA turnover. Gene array analysis shows that 7.3% of the total genes analyzed exhibited a greater than 1.6-fold difference between the pseudopod and cell body fractions. Of these, only 13.2% (261 genes) are enriched in pseudopodia, suggesting that only a limited number of total cellular mRNAs are enriched in tumor cell protrusions. Comparison of the tumor pseudopod mRNA cohort and a cohort of mRNAs enriched in neuronal processes identified tumor pseudopod-specific signaling networks that were defined by expression of M-Ras and the Shp2 protein phosphatase. Pseudopod expression of M-Ras and Shp2 mRNA were diminished by ROCK inhibition linking pseudopodial Rho/ROCK activation to the localized expression of specific mRNAs. Pseudopodial enrichment for mRNAs involved in protein translation and signaling suggests that local mRNA translation regulates pseudopodial expression of less stable signaling molecules as well as the cellular machinery to translate these mRNAs. Pseudopodial Rho/ROCK activation may impact on tumor cell migration and metastasis by stimulating the pseudopodial translocation of mRNAs and thereby regulating the expression of local signaling cascades. Keywords: tumor cells, protrusive cellular domains, pseudopodia vs cell body, RNA trafficking
2008-10-17 | GSE13253 | GEO
Project description:mRNA trafficking and local protein translation are associated with protrusive cellular domains, such as neuronal growth cones, and deregulated control of protein translation is associated with tumor malignancy. We show here that activated RhoA, but not Rac1, is enriched in pseudopodia of MSV-MDCK-INV tumor cells and that Rho, Rho kinase (ROCK) and myosin II regulate the microtubule-independent targeting of RNA to these tumor cell domains. ROCK inhibition does not affect pseudopodial actin turnover but significantly reduces the dynamics of pseudopodial RNA turnover. Gene array analysis shows that 7.3% of the total genes analyzed exhibited a greater than 1.6-fold difference between the pseudopod and cell body fractions. Of these, only 13.2% (261 genes) are enriched in pseudopodia, suggesting that only a limited number of total cellular mRNAs are enriched in tumor cell protrusions. Comparison of the tumor pseudopod mRNA cohort and a cohort of mRNAs enriched in neuronal processes identified tumor pseudopod-specific signaling networks that were defined by expression of M-Ras and the Shp2 protein phosphatase. Pseudopod expression of M-Ras and Shp2 mRNA were diminished by ROCK inhibition linking pseudopodial Rho/ROCK activation to the localized expression of specific mRNAs. Pseudopodial enrichment for mRNAs involved in protein translation and signaling suggests that local mRNA translation regulates pseudopodial expression of less stable signaling molecules as well as the cellular machinery to translate these mRNAs. mRNA trafficking and local protein translation are associated with protrusive cellular domains, such as neuronal growth cones, and deregulated control of protein translation is associated with tumor malignancy. We show here that activated RhoA, but not Rac1, is enriched in pseudopodia of MSV-MDCK-INV tumor cells and that Rho, Rho kinase (ROCK) and myosin II regulate the microtubule-independent targeting of RNA to these tumor cell domains. ROCK inhibition does not affect pseudopodial actin turnover but significantly reduces the dynamics of pseudopodial RNA turnover. Gene array analysis shows that 7.3% of the total genes analyzed exhibited a greater than 1.6-fold difference between the pseudopod and cell body fractions. Of these, only 13.2% (261 genes) are enriched in pseudopodia, suggesting that only a limited number of total cellular mRNAs are enriched in tumor cell protrusions. Comparison of the tumor pseudopod mRNA cohort and a cohort of mRNAs enriched in neuronal processes identified tumor pseudopod-specific signaling networks that were defined by expression of M-Ras and the Shp2 protein phosphatase. Pseudopod expression of M-Ras and Shp2 mRNA were diminished by ROCK inhibition linking pseudopodial Rho/ROCK activation to the localized expression of specific mRNAs. Pseudopodial enrichment for mRNAs involved in protein translation and signaling suggests that local mRNA translation regulates pseudopodial expression of less stable signaling molecules as well as the cellular machinery to translate these mRNAs. Pseudopodial Rho/ROCK activation may impact on tumor cell migration and metastasis by stimulating the pseudopodial translocation of mRNAs and thereby regulating the expression of local signaling cascades. Keywords: tumor cells, protrusive cellular domains, pseudopodia vs cell body, RNA trafficking Pseudopod purification- Pseudopodia purification was performed as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005). Briefly, 107 MSV-MDCK-INV cells were plated on 100 mm 1um pore filters mounted between two 3-3.5â custom-made washers (Boulons Plus, Anjou, QC) in a 100 mm Falcon Petri dish and the exterior sealed with agarose to prevent cell leakage to the bottom of the filter. After 24 hours culture, the filter was washed 4 times with cold PBS containing 0.1 mM Ca2+ and 1 mM Mg2+ and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass cover slip in ice-cold lysis buffer (20 mM Tris-HCl pH 7.6, 0.5% NP-40, 250 mM NaCl, 3 mM EDTA, 3 mM EGTA containing freshly added 2 mM DTT, 0.5 mM PMSF, 1 mM sodium vanadate, 2.5 mM sodium fluoride and 1uM leupeptin). Affymetrix gene array- GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrge.ca). Six Affymetrix canine arrays (3 pseudopodia, 3 cell body) were scanned with the Affymetrix GeneChip Scanner 3000 and signal intensities for genes generated with GCOS1.2 (Affymetrix Inc., Santa Clara, CA) using default values for statistical expression algorithm parameters, a target signal of 150 for all probe sets and a normalization value of 1. To determine significant differences in gene expression levels between pseudopodia and cell body samples, 1 way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 6 samples.
2010-05-18 | E-GEOD-13253 | biostudies-arrayexpress
Project description:Regulated local translation, RNA transport and protein localization are critical for spatio-temporal gene expression in neurons. The localization of mRNA and subsequent local protein synthesis contribute to neuronal functions like synaptogenesis, synapse pruning, axon guidance, axonal regeneration and synaptic plasticity. Thus, mutations in motor proteins and subsequent cargo transport failure lead to motoneuron diseases. The kinesin family member 1 C has been shown to play a role in different cargo transport alongside the microtubule network, but the pathomechanisms behind KIF1C deficiency mediated motoneuron diseases has not been deciphered yet. Additionally, the exon junction complex has been suggested as a molecular link between splicing and cytoplasmic mRNA localization and local translation. Here we identified KIF1C as a EJC transporter in neuronal cells. We investigated the KIF1C proteome in differentiated SH-SY5Y cells and found an interaction of KIF1C with EJC components and other RNA-binding proteins in KIF1C overexpressing SH-SY5Y cells. The interaction could be validated via immunoprecipitation and an endogenous eIF4A3 co-immunoprecipitation. The co-localization of eIF4A3 and RBM8A with wildtpye KIF1C at protrusions of SH-SY5Ys further confirms the interaction. The mislocalization of eIF4A3 and RMB8A due to KIF1C mutation suggests a transport of the EJC by KIF1C. Furthermore, the interaction of KIF1C with PABPC1 and EJC components is RNA mediated. We additionally demonstrate via complex capture with KIF1C overexpressing HEK293 cells that KIF1C interacts with RNA itself. We therefore suggest the interaction of KIF1C not only with the EJC, but with a complex containing RNA and the EJC. Hence KIF1C is a transporter of mRNA and the EJC.
2023-12-28 | PXD037387 | Pride
Project description:We generated fibroblast lines overexpressing beta-globin constructs under a doxycycline-inducible promoter. These constructs contain the beta-globin coding sequence followed by either a control 3'UTR (HBB) or the Pkp4 3'UTR. The Pkp4 3'UTR carries a protrusion-targeting element and is expected to compete with localization of endogenous protrusion-localized mRNAs. We used a fractionation scheme to isolate protrusions and cell bodies from HBB and Pkp4 UTR-expressing fibroblasts, which were induced to extend protrusions in response to addition of lysophosphatidic acid (LPA). 4 replicate protrusion and cell body samples for each cell type were analyzed by RNA-Seq. To identify RNAs enriched in protrusions, a protrusion/cell body ratio was calculated. We find that ca. 4.5% of detected RNAs were enriched in protrusions of control HBB cells. Overexpression of the Pkp4 UTR reduced the protrusion enrichement of a subset of these RNAs, while the degree of localization of the remaining RNAs was not significantly affected.
2017-10-11 | GSE82230 | GEO
Project description:We used a fractionation scheme to isolate protrusions and cell bodies from control or APC knockdown fibroblasts, which were induced to extend protrusions in response to addition of lysophosphatidic acid (LPA). Four replicate protrusion and cell body samples for each cell type were analyzed by RNA-Seq. To identify RNAs enriched in protrusions, a protrusion/cell body ratio was calculated. We find that ca. 7% of detected RNAs were enriched in protrusions of control cells. Knockdown of APC reduced the protrusion enrichement of a subset of these RNAs, indicating that they are dependent on APC for their localization. Localization of the remaining RNAs was not significantly affected upon APC knockdown suggesting that their localization is mediated by an APC-independent mechanism.
2017-10-11 | GSE82229 | GEO