Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of cell membrane proteins involved in dsRNA internalization

ABSTRACT: Cellular uptake of dsRNA from the environment is a widespread phenomenon among insects. In Drosophila and in honeybees, the injection and the ingestion respectively of dsRNA against a viral sequence is sufficient to hinder virus replication. We wanted to identify cell surface proteins that bind to extracellular dsRNA, mediating its internalization. To this end, we developed an unconventional co-immunoprecipitation protocol followed by proteomics analysis.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Drosophila Melanogaster (fruit Fly)

TISSUE(S): Cell Culture, Embryonic Stem Cell

SUBMITTER: Yann Verdier

LAB HEAD: Joelle Vinh

PROVIDER: PXD034508 | Pride | 2025-04-11

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	1150_1151_1152_1153.mzid.gz	Mzid
	December.msfView	Msf
	December.pdResult	Other
	December.xlsx	Xlsx
	F091849.mgf	Mgf

Items per page:

1 - 5 of 32

Similar Datasets

Cellular dsRNA interactome captured by K1 antibody reveals the regulatory map of exogenous RNA sensing

Project description:We developed an anti-dsRNA antibody co-immunoprecipitation coupled with quantitative mass spectrometry to comprehensively identify RBPs bound to cellular dsRNAs. To minimize false positives, we conducted a quantitative mass spectrometry analysis under two additional conditions: first, by treating the samples with RNase T1 to degrade single-stranded RNAs, and second, by performing a pull-down using synthetic double-stranded RNA, poly(I:C). The interactomes through these three methods provide an unbiased and thorough characterization of potential dsRBPs bound to cellular dsRNAs.

2025-02-03 | PXD053100 | Pride

Determination of dsRNA interactome upon Sindbis virus infection in human cells identifies SFPQ as a critical proviral factor

Project description:Viruses are obligate intracellular parasites, which depend on the host cellular machineries to replicate their genome and complete their infectious cycle. Long double stranded (ds)RNA is a common viral by-product originating during RNA virus replication, which is universally sensed as a danger signal to trigger the antiviral response. As a result, viruses hide dsRNA intermediates into viral replication factories and have evolved strategies to hijack cellular proteins for their benefit. The characterization of the host factors associated to viral dsRNA and involved in viral replication remains a major challenge to develop new antiviral drugs against RNA viruses. Here, we performed anti-dsRNA immunoprecipitation followed by Mass Spectrometry to fully characterize the dsRNA interactome in Sindbis virus (SINV) infected human HCT116 cells. Among the validated factors, we characterized SFPQ (Splicing factor, proline-glutamine rich) as a new dsRNA-associated factor upon SINV infection. We proved that SFPQ is able to directly bind dsRNAs in vitro, that SFPQ association to dsRNA is independent on single-stranded (ss)RNA flanking regions in vivo and that it is able to bind the viral genome upon infection. Furthermore, we showed that either knock-down or knock-out of SFPQ reduced SINV infection in human HCT116 and SKNBE cells, suggesting that SFPQ could enhance viral replication. Overall, this study not only represents a resource to further study SINV dsRNA-associated factors upon infection but also identifies SFPQ as a new proviral dsRNA binding protein.

2024-05-22 | PXD024554 | Pride

Integrative structural analysis of NF90-NF45 heterodimers reveals architectural rearrangements and oligomerisation on binding dsRNA

Project description:EDC Crosslinking Mass Spectrometry with quantitation of NF90-NF45 protein complex and NF45-NF90long-dsRNA complex

2025-05-07 | PXD053010 | Pride

Genes affected upon dsRNA knockdown treatment for nbr/CG9247 in Drosophila DL1 cells

Project description:nbr/CG9247 gene function regulates the length of the 3'end of miRNAs. Such 3'end heterogeneity of miRNAs may impact miRNA target gene silencing. To address this, we performed microarray analysis for genes altered upon nbr knockdown in Drosophila DL1 cells. This approach revealed a subset of genes upregulated upon nbr knockdown. Five independent replicates of DL1 cells treated with control (dsRNA to renilla) or nbr (dsRNA RNA to nbr/CG9247) were collected 5 days after dsRNA bathing. Total RNA from from each replicate was extracted using TRIzol reagent (Invitrogen). A portion of total RNA for each replicate was used to confirm the effect of nbr knockdown on one of the nbr-dependent miRNAs, miR-34, by small RNA northern.

2011-11-01 | E-GEOD-32683 | biostudies-arrayexpress

Larval application of sodium channel homologous dsRNA restores pyrethroid insecticide susceptibility in a resistant adult mosquito population

Project description:Mosquitoes host and pass on to humans a variety of disease-causing pathogens such as infectious viruses and other parasitic microorganisms. The emergence and spread of insecticide resistance is threatening the effectiveness of current control measures for common mosquito vector borne diseases, such as malaria, dengue and Zika. Therefore, the emerging resistance to the widely used pyrethroid insecticides is an alarming problem for public health. Among the new approaches implemented for pest control, one of the most promising is RNA interference (RNAi). The aim of this study was to provide a feasible RNAi solution that can be applied on wild pyrethroid resistant mosquito populations in the near future. To achieve this, high dsRNA efficacy at economic quantities is required. It is recognized that the sodium channel transcript variability governs its functional diversity including the emergence of insecticide resistance. Therefore, to maximize the RNAi effect, we tiled a number of overlapping dsRNA constructs that together target about half of the voltage-gated sodium channel (VGSC) transcript variants annotated in this work. This strategy provided a refined dsRNA trigger that increased mortality with a three-fold decrease in dsRNA amounts compared to the primary VGSC dsRNA construct. Thus, we demonstrated the use of RNA interference (RNAi) to increase susceptibility of adult mosquitoes to a widely used pyrethroid insecticide. Small RNA sequences from 5 mosquitoes treated with Random or VGSC dsRNAs were generated using Illumina HiSeq 2500.

2016-07-06 | E-GEOD-84030 | biostudies-arrayexpress

Expressed dsRNA provokes selective sequence-independent PKR response in transient co-transfection experiments

Project description:In mammals, double-stranded RNA (dsRNA) plays roles in sequence-specific RNA interference, sequence-independent interferon response, and RNA editing by adenosine deaminases. We have previously shown that long hairpin dsRNA expression in cultured cells does not activate the interferon response, it is poorly processed into siRNAs, and it is partially edited. Here, we demonstrate that dsRNA expressed from transiently transfected plasmids strongly inhibits expression of co-transfected reporter plasmids but not expression of endogenous genes or reporters stably integrated in the genome. The inhibition is concentration-dependent and independent of a cell type, transfection method, or dsRNA sequence. The inhibition occurs at the level of translation and is mediated by protein kinase R (PKR). PKR binds the expressed dsRNA, becomes phosphorylated and changes its distribution along polysome fractions. In conclusion, we demonstrate that expression from plasmids is selectively repressed if one of co transfected plasmids produces dsRNA. Our results highlight the importance of proper controls and careful interpretation of co-transfection experiments. HEK293 cells (human origin) were transiently transfected with hairpin dsRNA-expressing (MosIR) and control (pCag) plasmids.

2013-12-27 | E-GEOD-46959 | biostudies-arrayexpress

RNAi profiling of Drosophila Schneider S2 cells treated with dsRNA vs. GFP

Project description:Cis-natural antisense transcripts (cis-NATs) have been speculated to be substrates for endogenous RNA interference (RNAi), but little experimental evidence for such a pathway in animals has been reported. Analysis of massive Drosophila melanogaster small RNA data sets now reveals that endogenous small interfering RNAs (siRNAs) are produced via bidirectional transcription. >100 cis-NATs with overlapping 3' exons generate 21-nt, Dicer-2 (Dcr-2)Âdependent, 3'-end modified siRNAs. To determine whether any co-expressed cisNATs are denied entry into the RNAi pathway, we analyzed the gene expression profile of S2 cells. The analysis suggested that the processing of cis-NATs by RNAi are actively restricted, and the selected loci are enriched for nucleic acidÂbased functions and include Argonaute-2 (AGO2) itself. Experiment Overall Design: Drosophila Schneider cells (S2) were treated with dsRNA against GFP for 8 days. The treatment was done in duplicate. Total RNA was extracted from the dsRNA treated cells using trizol. Experiment Overall Design: Gene expression analysis was conducted using Drosophila Genome 2.0 GenechipÂ® arrays (Affymetrix, Santa Clara, CA). Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3Â¹ Amplification One-Cycle Target labeling kit according to manufacturerÂ¹s protocol. For each array, 10ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450. Arrays were then scanned with an Affymetrix Scanner 3000 and data was obtained using the GenechipÂ® Operating Software (Version 1.2.0.037).

2008-06-20 | E-GEOD-11370 | biostudies-arrayexpress

Single-cell RNA-seq of of human dermal fibroblasts (supplementary - different stimulation conditions of dsRNA)

Project description:Dermal fibroblasts from one human individual were stimulated with dsRNA (poly I:C) in a time course of 2,4 and 6 hours. In one time course - the dsRNA was removed after 30mins, in a second time course it was removed after 1 hour, while in the third the dsRNA was kept in medium for the entire time course. Following collection, cells were profiled using the Smart-seq2 protocol.

2018-07-16 | E-MTAB-7052 | biostudies-arrayexpress

unclassified dsRNA viruses

Project description:unclassified dsRNA viruses

| PRJNA16954 | ENA

Genes affected upon dsRNA knockdown treatment for nbr/CG9247 in Drosophila DL1 cells and small RNA profiling in Drosophila wild-type and nbr[f02257] mutants

Project description:This SuperSeries is composed of the following subset Series: GSE32683: Genes affected upon dsRNA knockdown treatment for nbr/CG9247 in Drosophila DL1 cells GSE32684: Small RNA profiling in Drosophila wild-type and nbr[f02257] mutants Refer to individual Series

2011-11-01 | E-GEOD-32564 | biostudies-arrayexpress