Total RNAseq of sfpq sibling (+/+, +/-) and null (-/-) primary zebrafish neuron cellular and neurite tissue
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ABSTRACT: Zebrafish primary neurons either sfpq sibling/control (+/+, +/-) or null (-/-) were cultured in transwell inserts. At DIV2, for each genotype, cellular and neurite tissues were separately isolated, RNA extracted and total RNAseq performed.
Project description:We report mRNA profiles of subcellularly localized transcriptomes (soma and neurite) of two mouse cell lines, N2A and CAD, as well as primary cortical neurons from E18.5 mice. We also performed this fractionation and sequencing after RNAi knockdown (cell lines) or in knockout mice (primary cortical neurons) of the RNA-binding proteins muscleblind 1 and 2 (Mbnl1 and Mbnl2). Fractionate neurons using porous transwell membranes. Isolate poly-A RNA.
Project description:Phenotypic characterisation of our zebrafish sfpq homozygous mutants revealed a restricted set of specific defects, unexpected for a protein expressed ubiquitously and involved in such general mechanisms. The CNS was prominently affected, showing brain boundary and axonal defects associated with absence of motility. To investigate a possible specificity in SFPQ functional targets by microarray RNA profiling analysis, comparing the transcriptome of the sfpq homozygous mutants with its wild type and heterozygous siblings at the earliest stage at which the phenotype is robustly recognizable.
Project description:The goal of this study was to analyse the effects of the SFPQ-TFE3 fusion by transforming kidney tubuloids with the construct. Samples without the construct (luciferase only) and overexpressing the partner only (TFE3) were also used as controls. Furthermore, transformed organoids were also transferred into mice PDX models to check their tumorigenic potential; tumors derived from the organoids were subsequently used for sequencing.
Project description: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.
Project description:Analysis of SFPQ interactome in primary melanocytes and melanoma cells. Results provide insight into the oncogenic reprogamming of SFPQ-RNA interactome and especially the interactions with key melanoma-associated coding transcripts.
Project description:We identified the major RNA binding protein-SFPQ as a direct interaction partner of FTO. Our study showed that FTO and SFPQ were located in close proximity throughout the transcriptome and overexpression of SFPQ led to the demethylation of adjacent N6-methyladenosine on RNA
Project description:Loss of TGF-beta growth-inhibitory responses is a hallmark of human cancer. However, the molecular mechanisms underlying the TGF-beta resistance of cancer cells remain to be fully elucidated. Splicing factor proline- and glutamine-rich protein (SFPQ) is a prion-like RNA-binding protein that is frequently upregulated in human cancers, such as Hepatocellular carcinoma (HCC). In this study, we identified SFPQ as a potent suppressor of TGF-beta signaling. The ability of SFPQ to suppress TGF-beta responses depended on its prion-like domain (PrLD) that drives phase separation (LLPS). Mechanistically, SFPQ physically restrained Smad4 in its condensates, which excluded Smad4 from the Smad complex and chromatin occupancy, and thus functionally dampened Smad-dependent transcriptional responses. Accordingly, SFPQ deficiency or loss of LLPS rendered cells hypersensitive to TGF-beta responses. Together, our data reveal a unique function of SFPQ through LLPS that suppresses Smad transcriptional activation and TGF-beta tumor-suppressive activity.
Project description:SFPQ is a multifunctional nuclear protein first identified as a splicing factor, that participates in several cellular activities, including RNA transport, apoptosis and DNA repair. Here we report that SFPQ is a key mediator of platinum sensitivity in Epithelial Ovarian Cancer cell lines.