Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Unconventional RNA-binding proteins in mitosis

ABSTRACT: Ribonucleoprotein complexes are dynamic assemblies of RNA associated with RNA-binding proteins (RBPs), which can modulate the fate of the RNA molecules from transcription to degradation. Dysregulation of RBPs is linked to diseases such as cancer and neurological disorders, which motivated the development of multiple approaches to catalog RBPs. RNA and RBPs are present in mitotic structures like the centrosomes and spindle microtubules, but their influence on mitotic spindle integrity remains unknown. The unconventional RNA-binding protein AURKA is investigated. Mass spectrometry analysis was used to identify AURKA RNA-dependent interaction partners.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Hela Cell

SUBMITTER: Maiwen Caudron-Herger

LAB HEAD: Maïwen Caudron-Herger

PROVIDER: PXD056233 | Pride | 2025-02-25

REPOSITORIES: pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	UP000005640_9606.fasta	Fasta
	mqpar.xml	Xml
	oecf3-VR0536-01.raw	Raw
	oecf3-VR0536-02.raw	Raw
	oecf3-VR0536-03.raw	Raw

Items per page:

1 - 5 of 36

Similar Datasets

Characterising the RNA-binding protein atlas of the mammalian brain uncovers RBM5 misregulation in mouse models of Huntington’s disease

Project description:RNA-binding proteins (RBPs) are key players regulating RNA processing and are associated with disorders ranging from cancer to neurodegeneration. Here, we present a proteomics workflow for large-scale identification of RBPs and their RNA-binding regions in the mammalian brain identifying 526 RBPs including 86 previously undescribed. Analysing brain tissue from the Huntington’s disease (HD) R6/2 mouse model uncovered differential RNA-binding of the alternative splicing regulator RBM5. Combining several omics workflows, we show that RBM5 binds differentially to transcripts enriched in pathways of neurodegeneration in R6/2 brain tissue. We further find these transcripts to undergo changes in splicing and demonstrate that RBM5 directly regulates these changes in human neurons derived from embryonic stem cells. Finally, we reveal that RBM5 interacts differently with several known huntingtin interactors and components of huntingtin aggregates. Collectively, we demonstrate the applicability of our method for capturing RNA interactor dynamics in the contexts of tissue and disease.

2023-06-22 | PXD029227 | Pride

Cisplatin induces the rearrangement of RBPs on CDKN1B/p27 mRNA

Project description:Cisplatin (CP) is a chemotherapeutic drug that is used to cure different types of cancer. CP induces DNA damage and leads to cell cycle arrest. The cyclin-dependent kinase inhibitor 1B (CDKN1B), also termed p27, plays an important role in the drug response ; and increased levels of p27 correlated with CP resistance. In HEK293 cells, we observed that p27 mRNAs levels increased whereas protein level drastically decreased in cells treated with CP; suggesting post-transcriptional regulatory events. To further understand the underlying mechanisms, we applied a biochemical approach combined with mass-spectrometry to systematically identify the RNA-binding proteins (RBPs) that are bound to the 3’UTR of p27 mRNAs in CP-treated versus non-treated cells in vivo. We found that 24 proteins, most of them known RBPs such HuR, hNRNPD, changed their association with p27 mRNA upon CP treatement. Furthermore, knock-down of a subset of the identified RBPs led to the inhibition of the CP-induced increase of p27 mRNA levels. In conclusion, these results highlight substantial rearrangement between RBPs and p27 mRNA upon CP treatment and corroborate the importance of post-transcriptional control in cellular drug response.

2019-09-27 | PXD008498 | Pride

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

Kinesin-associated RNA: RNA co-immunoprecipitated with Kinesin IP vs RNA from Aplysia CNS

Project description:Whole genome transcriptional profiling is used to identify ESTs found in RNA co-immunoprecipitated from Aplysia CNS with antibodies against Aplysia Kinesin Heavy Chain (ApKHC) RNA derived from Aplysia CNS served as control in the opposite channel. Custom Aplysia EST array to probe the samples was designed and ordered from Agilent. Two-condition experiment; four biological replicates for each condition were reciprocally hybridized on each two-color array

2013-04-26 | E-GEOD-30386 | biostudies-arrayexpress

Enhanced RNA interactome capture (eRIC) of human malignant bone tumor cells and normal bone/mesenchymal cells

Project description:Patient-derived bone tumor (osteosarcoma and giant cell tumor of bone) cells, and the normal mesenchymal stem cells and osteoblasts were cultured and subjected to UV crosslinking (UV) at 254 nm or without crosslinking (noUV) as negative controls. Subsequently, RNA-binding proteins (RBPs) were identified by eRIC.

2024-02-28 | PXD038185 | Pride

Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein

Project description:RNA-binding proteins (RBPs) play important roles in bacterial gene expression and physiology but their true number and functional scope remain little understood even in model microbes. To advance global RBP discovery in bacteria, we here establish glycerol gradient sedimentation with RNase treatment and mass spectrometry (GradR). Applied to Salmonella enterica, GradR confirms many known RBPs by their RNase-sensitive sedimentation profiles, and discovers the FopA protein as a new member of the emerging family of FinO/ProQ-like RBPs. FopA, encoded on resistance plasmid pCol1B9, primarily targets a small RNA associated with plasmid replication. The target suite of FopA dramatically differs from the related global RBP ProQ, revealing context-dependent selective RNA recognition by FinO-domain RBPs. Numerous other unexpected RNase-induced changes in gradient profiles suggest that cellular RNA helps to organize macromolecular complexes in bacteria. By enabling poly(A)-independent generic RBP discovery, GradR provides an important element for building a comprehensive catalogue of microbial RBPs.

2020-07-16 | PXD018422 | Pride

A new world of RNA-binding proteins in heterocyst-forming cyanobacteria.

Project description:RNA-binding proteins (RBPs) are central components of gene regulatory networks and RNA metabolism. The differentiation of nitrogen-fixing heterocysts in some filamentous cyanobacteria and their cooperation with vegetative cells in the same filament is one of the evolutionarily oldest cases of true multicellularity. Nostoc sp. PCC 7120 (Nostoc) is a model organism for filamentous cyanobacteria that differentiate heterocysts. Although hundreds of noncoding transcripts may be involved in this process, the RBPs that could cooperate with them are poorly characterized. We have used R-DeeP/GradR, a technique based on the differential sedimentation of RNA-protein complexes after RNase treatment in density gradients. All macromolecular complexes in the cell are fractionated by a sucrose gradient followed by high-resolution proteomics. We have compared gradients of RNase-treated with untreated samples in triplicates. If a protein was part of an RNA-protein complex, the complex should be disassembled after the RNase treatment and a shift of the protein position in the gradient should be observed (RNA-dependent proteins). Our approach yielded 333 RNA-dependent proteins. The results were compared to a bioinformatic prediction of RBPs and biochemical validation. We validated in vivo the RNA-binding capacity of 6 new RBPs. Some of these proteins were previously known to be involved in essential biological processes such as photosynthesis or heterocyst differentiation, but their association with RNA was previously unknown. In other cases, the function of the validated candidates was unknown. A knock-out strain of alr1700, a gene encoding a validated RNA-binding protein of unknown function, showed a deregulation of heterocyst differentiation, confirming the role of RBPs in regulating this cell differentiation process.

2024-11-08 | PXD050404 | Pride

Effects of deletion of genes encoding RNA-binding proteins on gene expression in S. pombe

Project description:To study the contribution of RNA-binding proteins (RBPs) to the regulation of RNA turnover, we used DNA microarrays to examine the transcriptome of S. pombe strains containing deletions in non-essential genes encoding RBPs

2014-11-06 | E-MTAB-2314 | biostudies-arrayexpress

Tranposable elements modulate human mRNAs and lncRNAs via specific RNA-protein interactions.

Project description:Transposable elements (TEs) have significantly influenced the evolution of transcriptional regulatory networks in the human genome. Post-transcriptional regulation of human genes by TE-derived sequences has been observed in specific contexts, but has yet to be systematically and comprehensively investigated. Here, studied a collection of CLIP-Seq (CrossLinked ImmunoPrecipitation) experiments mapping the RNA binding sites for a diverse set of 46 human proteins across 68 experiments to explore the role of TEs in post-transcriptional regulation genome-wide via RNA-protein interactions. We detected widespread interactions between RNA binding proteins (RBPs) and various families of TE-derived sequence in the CLIP-Seq data. Alignment coverage clustered on specific positions of the TE consensus sequences, illuminating a diversity of TE-specific motifs for many RBPs. Evidence of binding and conservation of these motifs in the nonrepetitive transcriptome suggest that TEs have appropriated existing sequence preferences of the RBP. Upon depletion of the RBPs, transcripts possessing TE-derived binding sites were similarly regulated as those bound in nonrepetitive sequence. However, in a few cases the effect of RBP binding depended on the specific TE family boundM-bM-^@M-^Te.g., the ubiquitously expressed RBP HuR conferred opposite effects on stability to transcripts when bound to Alu elements versus other families. Our meta-analysis suggests a widespread role for TEs in shaping RNA-protein regulatory networks in the human genome. HuR formaldehyde RIP-Seq in K562 cells, with RIP and input sequenced in triplicate.

2014-09-10 | E-GEOD-61238 | biostudies-arrayexpress

β-actin RNA-BioID

Project description:Function and fate of mRNAs is controlled by RNA binding proteins (RBPs) but determining the proteome of a specific mRNA in vivo is still challenging. RNA proximity biotinylation on the transported β-actin mRNA tagged with MS2 aptamers (RNA-BioID) is used to characterize the dynamic proteome of the β-actin mRNP in mouse embryonic fibroblasts (MEFs). We have identified > 60 β-actin associated RBPs including all six previously known as well as novel interactors. By investigating the dynamics of the β-actin mRNP in MEFs, we expand the set of β-actin mRNA associated RBPs and characterize the changes of the interacting proteome upon serum-induced mRNA localization. We report that the KH-domain containing protein FUBP3 represents a new β-actin associated RBP that binds to its 3’-untranslated region outside the known RNA localization element but is required for β-actin RNA localization. RNA-BioID will allow to obtain a dynamic view on the composition of endogenous mRNPs.

2020-03-12 | PXD010694 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data