Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SFPQ interacted proteins in HEK293T nucleus and cytoplasm

ABSTRACT: Splicing factor proline and glutamine rich (SFPQ), DNA- and RNA binding protein, is crucial in various nuclear processes, including paraspeckle formation, miRNA synthesis and specially in transcription regulation. In addition, SFPQ play a role in the innate immune response to viruses, including DNA and RNA viruses. However, the connections between SFPQ and EMCV infection remain unclear. Here we report that the SFPQ is essential for EMCV replication. Depletion of SFPQ impairs EMCV production, while forced expression of SFPQ could promote viral replication. Mechanistically, EMCV inhibited viral RNA-mediated type I IFN and IL6 production to eliminate host antiviral immune responses. Cellular SFPQ was cleaved by the EMCV proteinase then entered the cytoplasm and interacted with other ribosomal proteins to facilitate its internal ribosome entry site (IRES)-dependent translation. Moreover, loss of SFPQ may impress host translation related gene expression and thus facilitate the EMCV replication. Altogether, our work provides a possible target for resisting EMCV or EMCV-like virus’s infection.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell

SUBMITTER: Bin Zhou

LAB HEAD: Feng Qian

PROVIDER: PXD011865 | Pride | 2019-01-10

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Orbi06211_LYH-QF-ZB-nuclear.msf	Msf
	Orbi06211_LYH-QF-ZB-nuclear.raw	Raw
	Orbi06212_LYH-QF-ZB-cytoplasmic.msf	Msf
	Orbi06212_LYH-QF-ZB-cytoplasmic.raw	Raw

Items per page:

1 - 4 of 4

Similar Datasets

lnc-EAPV binding proteins in C57BL/6J BMDMs

Project description:Endogenous retroviruses (ERVs) are transposable elements that cause host genome instability and usually play deleterious roles such as tumorigenesis. Recent advances also suggest that this 'enemy within' may encode viral mimic to induce antiviral immune responses through viral sensors. Here, through whole genome RNA-seq we discovered a full-length ERV-derived long non-coding RNA (lncRNA), designated lnc-EPAV (ERV-derived lncRNA positively regulates antiviral responses), as a positive regulator of NF-κB signaling. Lnc-EPAV expression was rapidly up-regulated by viral RNA mimic or RNA viruses to facilitate the expression of RELA, an NF-κB subunit that plays a critical role in antiviral responses. In turn, RELA promoted the transcription of lnc-EPAV to form a positive feedback loop. Transcriptome analysis of lnc-EPAV-silenced macrophages, combined with gain- and loss-of-function experiments, showed that lnc-EPAV was critical for induction of type I interferon (IFN) and inflammatory cytokine expression by RNA viruses. Consistently, lnc-EPAV-deficient mice exhibited reduced expression of type I IFNs, and consequently increased viral loads and mortality following lethal RNA virus infection. Mechanistically, lnc-EPAV promoted expression of RELA by competitively binding to and displacing SFPQ, a transcriptional repressor of RELA. The binding between ERV-derived RNAs and SFPQ also existed in human cells. Altogether, our work demonstrates an alternative mechanism by which ERVs regulate antiviral immune responses.

2018-11-07 | PXD011577 | 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

RNAi knock down of dU2AF50 in Drosophila mel2 cells and profiling of nuclear and cytoplasmic fractions

Project description:Nuclear and cytoplasmic RNA were extracted by hypotonic cell lysis from D.-mel2 cell knock down by RNAi against dU2AF50 or with non-specific dsRNA.

2007-07-05 | E-GEOD-1344 | biostudies-arrayexpress

ATAD5 regulates R-loop by maintaining RNA helicase level and unloading PCNA at the replication fork

Project description:R-loops are formed when replicative forks collide with the transcriptional machinery and can cause genomic instability. However, it is unclear how R-loops are regulated at transcription-replication conflicts (TRC) sites and how replisome proteins are regulated to prevent R-loop formation or mediate R-loop tolerance. Here, we report that ATAD5, a PCNA unloader, plays dual functions to reduce R-loops both under normal and replication stress conditions. ATAD5 interacts with RNA helicases such as DDX1, DDX5, DDX21 and DHX9 and increases the abundance of these helicases at replication forks to facilitate R-loop resolution. Depletion of ATAD5 or RNA helicases consistently increases R-loops during the S phase and reduces the replication rate, both of which are enhanced by replication stress. In addition to R-loop resolution, ATAD5 prevents the generation of new R-loops behind the replication forks by unloading PCNA which, otherwise, accumulates and persists on DNA, causing a collision with the transcription machinery. Depletion of ATAD5 reduces transcription rates due to PCNA accumulation. Consistent with the role of ATAD5 and RNA helicases in maintaining genomic integrity by regulating R-loops, the corresponding genes were mutated or downregulated in several human tumors.

2021-09-09 | PXD018207 | Pride

Assessment of Kinome-wide Rewiring Upon Picornavirus Infection

Project description:Picornaviridae is a large family of single-stranded positive RNA viruses that can infect both humans and animals. These include the enteroviruses (e.g. poliovirus, coxsackievirus and rhinoviruses) as well as the cardioviruses (e.g. encephalomyocarditis virus (EMCV)). Picornaviruses have evolved to interact, use and/or evade cellular host systems to create the optimal environment for viral growth and spreading. It is known that these viruses can modify kinase activity during infection, but a comprehensive overview of the (de)regulation of cellular kinases during picornavirus infection is lacking. To study the landscape of kinase activity during picornavirus infection, we here applied dedicated targeted mass spectrometry-based assays targeting ~40% of the human kinome. Our data show that kinases of the MAPK pathways were activated (e.g. ERK1/2, RSK1/2, JNK1/2/3, p38), while kinase involved in regulating the cell cycle (e.g. CDK1/2, GWL, DYRK3) were inactivated. Additionally, we observed the activation of CHK2, an important kinase of the DNA damage response. Using pharmacological kinases inhibitors, we demonstrate that some of the activated kinases are essential for the replication of EMCV. Altogether, we provide a quantitative system-wide understanding of the regulation of kinome activity induced by picornavirus infection, which is important for developing novel therapeutic interventions.

2024-04-21 | PXD046598 | panorama

SFPQ depletion is synthetically lethal with BRAFV600E in colorectal cancer cells I

Project description:Oncoproteins such as the BRAFV600E kinase entrust cancer cells with malignant properties, but they also create unique vulnerabilies. Therapeutic targeting of the BRAFV600E-driven cytoplasmic signaling network has proven ineffective, since patients regularly relapse with reactivation of the targeted signaling pathways. Here, we identified the nuclear protein SFPQ to be synthetically lethal with BRAFV600E in a loss-of-function shRNA screen. SFPQ depletion decreased proliferation and induced apoptosis in BRAFV600E-driven colorectal and melanoma cells, and reduced tumor growth in xenografts. Mechanistically, SFPQ loss in BRAF-mutant cancer cells triggered the Chk1-dependent replication checkpoint, resulting in replication stress in the absence of overt DNA damage. Affected cells stalled in S-Phase with hallmark signs of impaired replication factories. Induction of BRAFV600E and concomitant loss of SFPQ sensitized cells to a combination of DNA replication checkpoint inhibitors and chemically induced replication stress, pointing towards future therapeutic approaches exploiting nuclear vulnerabilities induced by BRAFV600E.

2019-12-31 | GSE116631 | GEO

SFPQ depletion is synthetically lethal with BRAFV600E in colorectal cancer cells II

2020-04-27 | GSE149370 | GEO

Comparative proteomics of extracellular vesicles derived from wildtype or mutant EMCV-infected cells

Project description:Non-enveloped viruses, such as picornaviruses, can escape infected host cells via release in extracellular vesicles (EVs) prior to the induction of lysis. These EVs cloak the secreted virus particles in a host-derived membrane, which alters virus-host interactions that affect infection efficiency and antiviral immunity. Currently, little is known about the viral and host factors regulating the formation and release of EV-enclosed viruses. The encephalomyocarditis virus (EMCV), belonging to the family of picornaviruses, expresses a Leader protein that targets various host cell processes. In this study, LC-MS/MS proteomic analysis was performed on EVs isolated via density gradient-based separation from HeLa cells infected with wildtype or Leader-deficient EMCV. Proteomes of these EVs were compared and proteins incorporated in EVs in a Leader-dependent manner were subjected to functional enrichment analysis and protein-interaction analysis.

2022-06-02 | PXD033906 | Pride

MDA5 guards against infection by surveying cellular RNA homeostasis [II]

Project description:MDA5 is an innate immune RNA sensor that detects a range of viruses. MDA5’s RNA agonists are not well defined. We used individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP) to study its ligands. Surprisingly, upon infection with SARS-CoV-2 or encephalomyocarditis virus (EMCV), MDA5 bound overwhelmingly to cellular RNAs. Many binding sites were intronic and proximal to Alu elements. MDA5-bound RNA was enriched in Poly(A) and Poly(U) motifs, some of which may form double-stranded RNA. In EMCV-infected cells, cytoplasmic levels of intron-containing unspliced transcripts were increased, suggesting dysregulation of splicing. Concomitantly, MDA5 iCLIP peaks were enriched in introns accumulating in the cytoplasm of infected cells. Moreover, rescue of splicing abrogated MDA5 activation. Finally, depletion of viral RNA from RNA extracted from infected cells did not diminish its MDA5-stimulatory potential. Taken together, MDA5 surveys RNA processing fidelity and detects splicing perturbation during infection, establishing a paradigm of innate immune ‘guarding’ for RNA sensors.

2023-11-29 | GSE214663 | GEO

MDA5 guards against infection by surveying cellular RNA homeostasis [I]

2023-11-29 | GSE211240 | GEO