Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cytoplasmic ATRIP recuitment to centrosome

ABSTRACT: We fund that ATRIP was recruited to centrosomes, which mediated the hyperactivated centrosome maturation. Thus, to identify the centrosomal protein responsible for ATRIP centrosomal localization, we immunoprecipitated cytoplasmic ATRIP from G2-phase HeLa cells and analyzed the interactors by mass spectrometry. By disrupting ATRIP interactor, this aberrant process might be rescued, offering a potential therapy strategy.

ORGANISM(S): Homo Sapiens

SUBMITTER: Xuefeng Chen

PROVIDER: PXD073837 | iProX | Fri Jan 30 00:00:00 GMT 2026

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Similar Datasets

Gene expression profiling of neurons with Rbfox1 and Rbfox3 knockdown and rescue with cytoplasmic or nuclear Rbfox1 isoform [RNA-seq]

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 RNA-seq experiments. We performed RNA-seq to profile gene expression and splicing changes. The expression levels of Rbfox1 and Rbfox3 in cultured mouse hippocampal neurons were reduced by siRNAs. The reduction of Rbfox1 and 3 was rescued by expression of cytoplasmic or nuclear Rbfox1 splice isoform. The gene expression and splicing profiles were compared between different treatments. Eight samples were analyzed.

2015-12-10 | E-GEOD-71916 | biostudies-arrayexpress

An aberrant cytoplasmic intron retention programme is a blueprint for ALS-related RBP mislocalization

Project description:We recently described aberrant cytoplasmic SFPQ intron-retaining transcripts (IRTs) and concurrent SFPQ protein mislocalization as a new hallmark of amyotrophic lateral sclerosis (ALS). However the generalizability and potential roles of cytoplasmic IRTs in health and disease remain unclear. Here, using time-resolved deep-sequencing of nuclear and cytoplasmic fractions of hiPSCs undergoing motor neurogenesis, we reveal that ALS-causing VCP gene mutations lead to compartment-specific aberrant accumulation of IRTs. Specifically, we identify >100 IRTs with increased cytoplasmic (but not nuclear) abundance in ALS samples. Furthermore, these aberrant cytoplasmic IRTs possess sequence-specific attributes and differential predicted binding affinity to RNA binding proteins (RBPs). Remarkably, TDP-43, SFPQ and FUS - RBPs known for nuclear-to-cytoplasmic mislocalization in ALS - avidly and specifically bind to this aberrant cytoplasmic pool of IRTs, as opposed to any individual IRT. Our data are therefore consistent with a novel role for cytoplasmic IRTs in regulating compartment-specific protein abundance. This study provides new molecular insight into potential pathomechanisms underlying ALS and highlights aberrant cytoplasmic IRTs as potential therapeutic targets.

2020-12-31 | GSE152983 | GEO

Gene expression profiling of neurons with Rbfox1 and Rbfox3 knockdown and rescue with cytoplasmic or nuclear Rbfox1 isoform [RNA-seq]

2015-12-10 | GSE71916 | GEO

Mammalian RNA decay pathways are highly specialized and widely linked to translation

Project description:RNA decay is crucial for RNA turnover and surveillance, and misregulated in many diseases. This complex system is challenging to study, particularly in mammals, where it remains unclear whether decay pathways perform specialized or redundant roles. Cytoplasmic pathways, and links to translation, are particularly enigmatic. By directly profiling targets of decay factors (XRN1, SKIV2L and MTR4) and normal/aberrant translation events in mouse embryonic stem cells, we uncovered extensive specialization between decay pathways and crosstalk with translation. XRN1 (5’-3’) mediated cytoplasmic bulk mRNA turnover whereas SKIV2L (3’-5’) was universally recruited by ribosomes, tackling aberrant translation and sometimes modulating mRNA abundance. Further exploring translation surveillance, we identified AVEN and FOCAD as SKIV2L interactors. AVEN prevented ribosome stalls at structured regions, which otherwise required SKIV2L for clearance. This pathway was crucial for histone translation, uORF regulation and counteracting spurious non-coding RNA translation. In summary, we identified key targets, components and functions of mammalian RNA decay pathways, and uncovered extensive coupling to translation.

2020-01-29 | GSE134020 | GEO

Dynamic acetylation/deacetylation dictates TRIM27 nuclear-cytoplasmic localization for cancer progression

Project description:Dynamic acetylation/deacetylation dictates TRIM27 nuclear-cytoplasmic localization for cancer progression

| PRJNA1449926 | ENA

RNA-seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70

Project description:It has been recently shown that SNRNP70, a major component of the spliceosome, as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons, we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic-only human SNRNP70 (cyt-hSNRNP70). To understand the molecular function of the cytoplasmic pool of this splicing protein, we performed this RNA-seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that, we crossed heterozygous mutant animals that are also positive for the cyt-SNRNP70 transgene. We then split embryos into four groups: (i) sibling, (ii) siblings/cyt-hSNRNP70, (iii) null, (iv) null/cyt-hSNRNP70. Total RNA was extracted from each one of the four groups (three biological replicates per sample) and sequenced.

2022-10-31 | E-MTAB-12301 | biostudies-arrayexpress

Ataxin-2, Twenty-four and Dicer-2 are components of a non-canonical cytoplasmic polyadenylation complex

Project description:Cytoplasmic polyadenylation is a mechanism to promote mRNA translation in a wide variety of biological contexts. A canonical complex centered around the conserved RNA-binding protein family CPEB has been shown to be responsible for this process. We have previously reported evidence for an alternative non-canonical, CPEB-independent complex in Drosophila, of which the RNA-interference factor Dicer-2 is a component. Here, we investigate Dicer-2 mRNA targets and protein co-factors in cytoplasmic polyadenylation. Using RIP-Seq analysis we identify hundreds of novel Dicer-2 target transcripts, ~50% of which were previously found as targets of the cytoplasmic poly(A) polymerase Wispy, suggesting widespread roles of Dicer-2 in cytoplasmic polyadenylation. Large-scale immunoprecipitation revealed Ataxin-2 and Twenty-four among the high-confidence interactors of Dicer-2. Functional analysis indicate that both factors form an RNA-independent complex with Dicer-2, and are required for cytoplasmic polyadenylation of Dicer-2 targets. Our results reveal the composition of a novel cytoplasmic polyadenylation complex that operates during Drosophila early embryogenesis.

2022-08-29 | GSE189868 | GEO

C-type natriuretic peptide pre-maturation culture affects cytoplasmic maturation in bovine oocytes

Project description:C-type natriuretic peptide pre-maturation culture affects cytoplasmic maturation in bovine oocytes

| PRJNA1430792 | ENA

Somatic mutations of MLL4/COMPASS induce cytoplasmic localization providing insight into cancer prognosis and treatment

Project description:Cancer genome sequencing consortiums have recently catalogued an abundance of somatic mutations in the chromatin-modifying enzymes that regulate enhancer chromatin function across a wide range of human cancers. Defining the molecular mechanisms underlying the potential oncogenic function for these epigenetic mutations could serve as the basis for precision medicine approaches for cancer treatment. MLL4 (KMT2D) is a key histone lysine mono-methyltransferase within the COMplex of Proteins ASsociated with Set1 (COMPASS) family that regulates chromatin at enhancers, potentially functions as a tumor suppressor and is highly mutated in a large number of human cancers. We report that the mutations which cause MLL4 protein truncation also alter its subcellular localization, resulting in loss-of-function in the nucleus and gain-of-function in the cytoplasm. We demonstrate that isogenic correction of MLL4 truncation mutation rescues the aberrant localization phenotype and restores multiple MLL4 regulatory functions, including COMPASS integrity and stabilization, histone H3K4 mono-methylation, enhancer activation, and gene regulation. Moreover, isogenic correction diminishes the sensitivity of MLL4-mutated cancer cells to targeted metabolic inhibition. Using immunohistochemistry (IHC), we identified cytoplasmic MLL4 unique to the tissue of bladder cancer patients with MLL4 mutations. Using a preclinical carcinogen bladder cancer mouse model, we demonstrate that truncated, cytoplasmic MLL4 can be a biomarker for MLL4-mutated bladder cancers and predicts response to targeted metabolic inhibition therapy. We propose using the cytoplasmic MLL4 truncation phenotype as a prognostic marker in bladder cancer. We also highlight the broader potential for patient stratification based on MLL4 mutation status in MLL4 truncation diseases, including human cancers and Kabuki Syndrome.

2023-12-05 | GSE246058 | GEO

Inhibition of H3K9me3 induces cytoplasmic localization of histone H3 coupled with autophagy

Project description:Inhibition of H3K9me3 induces cytoplasmic localization of histone H3 coupled with autophagy

| PRJNA589615 | ENA