Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

STAU1 selectively regulates the expression of inflammatory and immune response genes and alternative splicing of nerve growth factor receptor signaling genes

ABSTRACT: STAU1 selectively regulates the expression of inflammatory and immune response genes and alternative splicing of nerve growth factor receptor signaling genes

PROVIDER: PRJNA563927 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10069431_1.fastq.gz	Fastqsanger.gz
	SRR10069431_2.fastq.gz	Fastqsanger.gz
	SRR10069432_1.fastq.gz	Fastqsanger.gz
	SRR10069432_2.fastq.gz	Fastqsanger.gz
	SRR10069433_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 9

Similar Datasets

STAU1 selectively regulates the expression of inflammatory and immune response genes and alternative splicing of nerve growth factor receptor signaling genes

Project description:To study the potential targets and functions of STAU1 which might be related to neuropathic pain, we obtained STAU1-regulated transcriptome in HeLa cells. High-throughput RNA sequencing(RNA-seq) were performed for HeLa cells and control cells to define the comprehensive gene expression profiles and identify the genome-wide alternative splicing events regulated by STAU1.

2020-10-20 | GSE136890 | GEO

STAU1 selectively regulates the expression of inflammatory and immune response genes and alternative splicing of the nerve growth factor receptor signaling pathway.

Project description:Double‑stranded RNA‑binding protein Staufen homolog 1 (STAU1) is a highly conserved multifunctional double‑stranded RNA‑binding protein, and is a key factor in neuronal differentiation. RNA sequencing was used to analyze the overall transcriptional levels of the upregulated cells by STAU1 and control cells, and select alternative splicing (AS). It was determined that the high expression of STAU1 led to changes in the expression levels of a variety of inflammatory and immune response genes, including IFIT2, IFIT3, OASL, and CCL2. Furthermore, STAU1 was revealed to exert a significant regulatory effect on the AS of genes related to the 'nerve growth factor receptor signaling pathway'. This is of significant importance for neuronal survival, differentiation, growth, post‑damage repair, and regeneration. In conclusion, overexpression of STAU1 was associated with immune response and regulated AS of pathways related to neuronal growth and repair. In the present study, the whole transcriptome of STAU1 expression was first analyzed, which laid a foundation for further understanding the key functions of STAU1.

| S-EPMC7551455 | biostudies-literature

3'READS+RIP defines differential Staufen1 binding to alternative 3'UTR isoforms and reveals structures and sequence motifs influencing binding and polysome association

Project description:Using 3ʹ region extraction and deep sequencing coupled to ribonucleoprotein immunoprecipitation (3’READS+RIP), together with reanalyzing previous STAU1 binding and RNA structure data, we delineate STAU1 interactions transcriptome-wide, including binding differences between alternative polyadenylation (APA) isoforms. Consistent with previous reports, RNA structures are dominant features for STAU1 binding to CDSs and 3ʹUTRs. Overall, relative to short 3ʹUTR counterparts, longer 3ʹUTR isoforms of genes have stronger STAU1 binding, most likely due to a higher frequency of RNA structures, including specialized IRAlus. However, a sizable fraction of genes express transcripts showing the opposite trend, attributable to AU-rich sequences in their alternative 3'UTRs, possibly recruiting antagonistic RBPs and/or destabilizing STAU1-binding RNA structures. Using STAU1-knockout cells, we show that strong STAU1 binding to mRNA 3'UTRs generally enhances polysome association. However, IRAlus have little impact on STAU1-mediated polysome association despite having strong interactions with the protein.

2020-11-05 | GSE148771 | GEO

Sciatic nerve crush regulation of RNA alternative poly-adenylation

Project description:Sciatic nerve crush regulation of RNA alternative poly-adenylation

| PRJNA962456 | ENA

Sciatic nerve crush regulation of ribosome-associated RNA in DRG neurons, alternative polyadenylation analytsis [DRGinjuryRiboTag2018-QuntSeq72h]

Project description:Nerve injury alters transcription and translational processes in cell-type specific manner.Here we probe the effect of sciatic nerve injury on alternative polyadenylation of ribosome associated RNA specifically in sensory neurons.Mice were subjected to crush of the sciatic nerve in one side, while the other nerve was spared and used as naive control condition.

2024-12-31 | GSE233823 | GEO

Monosome and disome profiling of Flag-STAU1 Flp-In 293 T-REx cells

Project description:Monosome and disome profiling was performed on Flag-STAU1 Flp-In 293 T-REx to study the causes of ribosomal collisions, and whether this may be modulated by the presence/absence of Staufen-1. Cells were treated with either an siRNA targeting STAU1 transcript (4x samples) or a control siRNA (2x samples). Two of the four samples treated with the STAU1 siRNA had siRNA-resistant STAU1 mRNA expression induced by doxycycline (rescue). Sequencing libraries from monosome and disome fractions were generated in parallel from the same samples. Note that unique molecular identifiers/random barcodes (UMIs/RBCs) were included in the sequencing experiment. Each UMI has been moved to the fastq read name of each read. For example \\"xxxxxxrbc:AGCCAAT\\" in the read name signifies that the given read had a UMI of \\"AGCCAAT\\". Using these UMIs, PCR duplicates can be removed with UMI-Tools following read alignment.

2023-04-30 | E-MTAB-9669 | biostudies-arrayexpress

Sciatic nerve crush regulation of RNA alternative poly-adenylation [DRGinjury_2019-QuantSeq_Rev_24h]

Project description:Sciatic nerve crush regulation of RNA alternative poly-adenylation [DRGinjury_2019-QuantSeq_Rev_24h]

| PRJNA978052 | ENA

A degradation motif in STAU1 defines a novel family of proteins involved in inflammation

Project description:Cancer development is regulated by inflammation. Staufen 1 (STAU1) is an RNA-binding protein whose expression level is critical in cancer cells as it is related to cell proliferation or cell death. STAU1 expression levels are downregulated during mitosis due to its degradation by the E3 ubiquitin ligase anaphase-promoting complex/cyclosome (APC/C). In this paper, we map the molecular determinant involved in STAU1 degradation in mitosis to amino acids 38-50 and, by alanine scanning, we shorten the motif to F39PxPxxLxxxxL50 (FPL-motif). Mutation of the FPL-motif prevents STAU1 degradation by APC/C. Interestingly, a search in databases reveals that the FPL-motif is shared by 15 additional proteins most of them being involved in inflammation. We show that one of these proteins, MAP4K1, is indeed degraded via the FPL-motif; however, it is not a target of APC/C. Using proximity labeling with STAU1, we identify TRIM25, an E3-ubiquitin ligase involved in the innate immune response and interferon production, as responsible for STAU1 and MAP4K1 degradation, dependent on the FPL-motif. These results are consistent with previous studies that linked STAU1 to cancer-induced inflammation and identify a novel degradation motif that likely coordinates a novel family of proteins involved in inflammation.

2023-02-21 | PXD037703 | Pride

A degradation motif in STAU1 defines a novel family of proteins involved in inflammation

2023-03-11 | PXD036675 | Pride

Sciatic nerve crush regulation of RNA alternative poly-adenylation

Project description:Poly-adenylation regulates post-transcriptional processing and localization of mRNA. To study the effect of nerve injury on poly-adenylation across the transcriptome, 3'-end RNAseq was carried on DRG neurons following sciatic nerve injury. Mice were subjected to crush of the sciatic nerve in one side, while the other nerve was spared and used as naive control condition.

2024-12-31 | GSE230721 | GEO

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