Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Profiling of CSDE1-bound RNAs under MKRN2-mediated ubiquitination

ABSTRACT: This study aims to elucidate how MKRN2-mediated ubiquitination regulates the RNA-binding capacity of CSDE1. By overexpressing CSDE1 in MKRN2 knockout (KO) SHSY5Y cells and complementing with MKRN2 for comparison, we systematically analyzed the alterations in the RNA-binding repertoire of CSDE1 upon its interaction with MKRN2.

ORGANISM(S): Homo sapiens

PROVIDER: GSE317793 | GEO | 2026/02/02

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Profiling of CSDE1-bound RNAs under MKRN2-mediated ubiquitination

Project description:Profiling of CSDE1-bound RNAs under MKRN2-mediated ubiquitination

| PRJNA1415271 | ENA

Identification of ubiquitination sites on protein CSDE1 in SHSY5Y cells.

Project description:This bottom-up proteomics dataset provides a global map of post-translational modifications (PTMs) on the RNA-binding protein CSDE1 in human neuroblastoma SHSY5Y cells. The data was acquired to survey the modification landscape of CSDE1, with a particular observation that lysine (K) residues displayed the most abundant modification signals among all amino acids. This unbiased survey informed subsequent functional studies investigating the role of specific modification sites. The relationship between CSDE1 and the E3 ligase MKRN2 was established in our prior research.

2026-03-02 | PXD073844 | Pride

MKRN2 physically interacts with GLE1 to regulate mRNA export and zebrafish retinal development

Project description:The canonical mammalian mRNA export process is thought to terminate at the cytoplasmic face of the nuclear pore complex through mRNP remodeling. We conducted a stringent affinity-purification mass-spectrometry-based screen of the physical interactions of human RNA-binding E3 ubiquitin ligases. The resulting protein-interaction network revealed unexpected interactions between the RNA-binding E3 ubiquitin ligase MKRN2 and GLE1, a DEAD-box helicase activator implicated in mRNA export termination. We assessed MKRN2 epistasis with GLE1 in a genetically tractable zebrafish model. Strikingly, morpholino-mediated knockdown or CRISPR/Cas9-based knockout of MKRN2 partially rescued retinal developmental defects seen upon GLE1 depletion. Next, using iCLIP, we showed that MKRN2 binds preferentially to the 3'UTR of a diverse subset of mRNAs. Next-generation sequencing of fractionated cell extracts revealed that nuclear export of MKRN2-associated mRNAs is enhanced upon knockdown of MKRN2. Taken together, these results indicate that MKRN2 selectively interacts with GLE1 to regulate mRNA nuclear export and retinal development.

2020-05-19 | GSE136399 | GEO

MKRN2 physically interacts with GLE1 to regulate mRNA export and zebrafish retinal development (RNA-Seq)

2020-05-19 | GSE136421 | GEO

The RNA-binding E3 ligase MKRN2 selectively disrupts IL-6 translation to restrain inflammation

Project description:Dysregulation of proinflammatory cytokine production leads to autoimmune and inflammatory diseases. Although E3 ligases and RNA-binding proteins (RBPs) are critical in autoimmunity and inflammation, whether RNA-binding E3 ligases (E3-RBPs) can regulate proinflammatory cytokine expression to be involved in autoimmune disorders remains unclear. Here, we found that MKRN2, an E3-RBP, selectively inhibits IL-6 expression in LPS-activated macrophages. MKRN2-deficient mice have increased IL-6 serum levels at the untreated stage or after LPS treatment, and exhibit increased severity of experimental colitis which is associated with increased IL-6 levels. MKRN2 is negatively correlated with IL-6 expression in clinical samples from patients with ulcerative colitis and rheumatoid arthritis. Mechanistically, upon encountering Il6 mRNA, MKRN2 links K29 polyubiquitin to Lys179 of PAIP1 which blocks PAIP1-eIF4A interaction, thus inhibiting the translational efficiency of Il6 mRNA. Our findings provide new mechanistic insight and potential therapeutic strategies for inflammatory autoimmune diseases by disrupting translation process of specific proinflammatory cytokines.

2025-04-27 | GSE289945 | GEO

iCLIP transcriptome-wide mapping of UNR (CSDE1) binding sites

Project description:Analysis of UNR (CSDE1) binding to RNA targets by iCLIP transcriptome-wide mapping.

2016-11-07 | E-MTAB-3818 | biostudies-arrayexpress

The RNA-binding E3 ligase MKRN2 selectively disrupts IL-6 translation to restrain inflammation [RNA-seq]

2025-04-27 | GSE291859 | GEO

Sciatic nerve injury-responsive differential CSDE1 association efficiency of ribosomal protein coding mRNAs

Project description:Gpr151 is an injury-responsive gene that promotes axon regeneration through its interaction with the 5'UTR region of its mRNA transcripts and the RNA-binding protein CSDE1. We found that knocking down or overexpressing the 5'UTR of Gpr151 changes the ribosomal protein mRNA regulon regulated by CSDE1. After the sciatic nerve injury, the association between the ribosomal protein mRNA regulon and CSDE1 was enhanced at dorsal root ganglions(DRGs), but this enhancement was not observed in the AAV-shGpr151 injected mice. Overexpression of 5'UTRmut, which has increased binding affinity to CSDE1, enhanced the ribosomal protein mRNA regulon and its association with CSDE1 in embryonic DRG neurons.

2023-08-18 | GSE236910 | GEO

Phosphorylation of CSDE1 drives ribosome interactions with implications for cancer malignancy

Project description:The RNA-binding protein CSDE1 is a key regulator of mRNA stability and translation in a broad spectrum of biological processes. We have previously shown that CSDE1 functions as an oncoprotein in melanoma, where it promotes invasion and metastasis, whereas it behaves as a tumour suppressor in squamous cell carcinoma, a tumor derived from keratinocytes. The reasons underlying these context-specific behaviours are unknown. To identify melanoma-specific vulnerabilities, we have compared CSDE1 protein isoforms and post-translational modifications in melanoma cells and keratinocytes, as well as in cells of different tumorigenic potential. Combining Nanopore sequencing with two-dimensional gel electrophoresis and proteomics, we identify one major CSDE1 isoform expressed in melanoma cells and patient samples and find that CSDE1 phosphorylation and interactions with ribosomes represent an early event in cellular transformation, correlating with changes in the subcellular localization of CSDE1. Our data show that CSDE1 phosphorylation promotes de novo interactions of CSDE1 with ribosomes, uncovering a specific vulnerability of melanoma cells that might be harnessed for therapeutic intervention.

2025-08-13 | GSE292019 | GEO

Unbiased identification of CSDE1-regulated targets during oncogene-induced senescence [RNA-Seq]

Project description:We show that the RNA-binding protein CSDE1/UNR promotes oncogene-induced senescence (OIS) in primary mouse keratynocytes challenged by over-expression of H-RASv12. Depletion of CSDE1 leads to senescence bypass, cell immortalization and tumor formation. Combining individual nucleotide cross-linking and immunoprecipitation (iCLIP), RNA-seq and polysome profiling followed by functional studies, we identify targets regulated by CSDE1 and uncover the downstream molecular mechanisms.

2022-01-11 | GSE159999 | 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