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Drosophila Imp iCLIP identifies an RNA assemblage co-ordinating F-actin formation

ABSTRACT: In this study, we employed a combination of RIP-seq and short- and long-wave iCLIP technologies to identify transcripts associated with cytoplasmic RNPs containing the RNA-binding protein Drosophila Imp. We also made a Imp knockdown vs luciferase control experiment.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE62997 | GEO | 2015/05/27

SECONDARY ACCESSION(S): PRJNA266435

REPOSITORIES: GEO

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Drosophila Imp iCLIP identifies an RNA assemblage co-ordinating F-actin formation

Project description:In this study, we employed a combination of RIP-seq and short- and long-wave iCLIP technologies to identify transcripts associated with cytoplasmic RNPs containing the RNA-binding protein Drosophila Imp. We also made a Imp knockdown vs luciferase control experiment. Two biological iCLIP-seq, as well as two mRNAseq made on cells harvested on the same day. Two biological PAR-iCLIP-seq. Two biological RIP-seq, as well as two mRNAseq made on cells harvested on the same day. Three biological mRNAseq of imp dsRNA treated cells as well as three control mRNAseq of cells treated with Luciferase dsRNA.

2015-05-27 | E-GEOD-62997 | biostudies-arrayexpress

Drosophila Imp iCLIP identifies an RNA assemblage coordinating F-actin formation.

Project description:BackgroundPost-transcriptional RNA regulons ensure coordinated expression of monocistronic mRNAs encoding functionally related proteins. In this study, we employ a combination of RIP-seq and short- and long-wave individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP) technologies in Drosophila cells to identify transcripts associated with cytoplasmic ribonucleoproteins (RNPs) containing the RNA-binding protein Imp.ResultsWe find extensive binding of Imp to 3' UTRs of transcripts that are involved in F-actin formation. A common denominator of the RNA-protein interface is the presence of multiple motifs with a central UA-rich element flanked by CA-rich elements. Experiments in single cells and intact flies reveal compromised actin cytoskeletal dynamics associated with low Imp levels. The former shows reduced F-actin formation and the latter exhibits abnormal neuronal patterning. This demonstrates a physiological significance of the defined RNA regulon.ConclusionsOur data imply that Drosophila Imp RNPs may function as cytoplasmic mRNA assemblages that encode proteins which participate in actin cytoskeletal remodeling. Thus, they may facilitate coordinated protein expression in sub-cytoplasmic locations such as growth cones.

| S-EPMC4477473 | biostudies-literature

E. coli imp fabI(G93V) Mutant Cells: Control (E. coli imp fabI(G93V) ) vs. NTG-treated E. coli imp fabI(G93V)

Project description:Transcriptional profiling of NTG-treated E. coli imp fabI(G93V) cells compared to control cells (E. coli imp fabI(G93V) ) in the absence or presence of sub-lethal concentration of triclosan.

2009-07-31 | GSE17441 | GEO

mRNP-mRNA Association Map (Tier I - G10, HuR, Imp, PABP)

Project description:In eukaryotic organisms gene regulatory networks require an additional level of coordination that links transcriptional and post-transcriptional processes. Messenger RNAs have traditionally been viewed as passive molecules in the pathway from transcription to translation. However, it is now clear that RNA-binding proteins play a major role in regulating multiple mRNAs in order to facilitate gene expression patterns. These tracks show the associated mRNAs that co-precipitated with the targeted RNA-binding proteins HuR, IMP-1 and PABP using RIP-Chip (Ribonomic) profiling Keywords: RIP-Chip For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

2009-01-24 | GSE14535 | GEO

Identification of Rbfox1 binding in the cytoplasm of neurons by iCLIP

Project description:Human genetic studies have identified the neuronal RNA binding protein, Rbfox1, as a candidate gene for autism spectrum disorders. While Rbfox1 functions as a splicing regulator in the nucleus, it is also alternatively spliced to produce cytoplasmic isoforms. To investigate cytoplasmic Rbfox1, we knocked down Rbfox proteins in mouse neurons and rescued with cytoplasmic or nuclear Rbfox1. Transcriptome profiling showed that nuclear Rbfox1 rescued splicing changes induced by knockdown, whereas cytoplasmic Rbfox1 rescued changes in mRNA levels. iCLIP-seq of subcellular fractions revealed that in nascent RNA Rbfox1 bound predominantly to introns, while cytoplasmic Rbox1 bound to 3' UTRs. Cytoplasmic Rbfox1 binding increased target mRNA stability and translation, and overlapped significantly with miRNA binding sites. Cytoplasmic Rbfox1 target mRNAs were enriched in genes involved in cortical development and autism. Our results uncover a new Rbfox1 regulatory network and highlight the importance of cytoplasmic RNA metabolism to cortical development and disease. In this data set, we included the data from iCLIP-seq experiments. We performed iCLIP procedures to identify Rbfox1 binding in the cytoplasm. Cultured mouse forebrain neurons were irradiated with UV and a cytoplasmic fraction was purified for immunoprecipitation. An anti-Rbfox1 antibody was used to immunoprecipitate Rbfox1 target RNAs and an anti-Flag antibody was used as control. Two samples were analyzed.

2015-12-10 | E-GEOD-71790 | biostudies-arrayexpress

mRNP-mRNA Association Map (Tier I - G10, HuR, Imp, PABP)

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Identification of Rbfox1 binding in the cytoplasm of neurons by iCLIP

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The long noncoding RNA Lnczc3h7a promotes TRIM25-mediated RIG-I antiviral innate immune response

Project description:In this study, we employed a combination of RIP-seq and iCLIP-seq technologies to identify long non-coding RNA associated with cytoplasmic TRIM25 and RIG-I protein in mouse macrophages cells.

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Self-recognition of an inducible host lncRNA by RIG-I feedback restricts innate immune response

Project description:In this study, we employed a combination of UV-RIP-seq, PacBio-seq and iCLIP-seq technologies to identify long non-coding RNA associated with cytoplasmic RIG-I protein in mouse macrophages cells.

2018-04-26 | GSE106254 | GEO

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