Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Total RNA Sequencing analysis of total RNA and RNA isolated from mitochondrial pellets in CSDE1-knockdown sensory neurons

ABSTRACT: CSDE1 is an RNA-binding protein that associates with a subset of mitochondria-related transcripts. We previously observed that RNAs encoding mitochondrial proteins localized to the mitochondrial inner membrane (MIM), intermembrane space (IMS), matrix, and outer membrane (MOM) are enriched within the CSDE1-bound RNA pool. To determine whether CSDE1 regulates the abundance and mitochondrial localization of mitochondria-associated RNAs in sensory neurons, we performed RNA sequencing of both total RNA and RNA extracted from isolated mitochondria isolated from CSDE1-knockdown sensory neurons. CSDE1 knockdown was achieved using lentiviral transduction, and sequencing results were compared with control neurons infected with empty vector (pLKO).

ORGANISM(S): Mus musculus

PROVIDER: GSE324285 | GEO | 2026/03/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

DRG tissue CSDE1-IP sequencing using sciatic nerve injured and uninjured mice.

Project description:To determine CSDE1 associated RNAs after injury in sensory neurons, we conducted CSDE1-IP sequencing analysis using dorsal root ganglion (DRG) tissues of wild type mice.

2025-09-01 | GSE301321 | GEO

polyA+ and total RNA sequencing profiling of UNR (CSDE1) knock down

Project description:Investigation of the effects of UNR (CSDE1) knock-down on transcript levels of Melanoma Cells.

2016-10-31 | E-MTAB-3805 | biostudies-arrayexpress

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

Csde1 binds transcripts involved in protein homeostasis and controls their expression in erythropoiesis

Project description:The RNA binding protein Csde1 (Cold shock domain protein e1) is strongly upregulated during erythropoiesis, but its expression is reduced in Diamond Blackfan Anemia (DBA). To understand the role of Csde1 in DBA, and the cellular pathways controlled by Csde1 in erythropoiesis, we identified the transcripts that physically associate with Csde1. These mainly encoded proteins involved in ribogenesis, mRNA translation and protein degradation, but also proteins associated with the mitochondrial respiratory chain and mitosis. Crispr/Cas9-mediated deletion of the first cold shock domain of Csde1 affected RNA expression and/or protein expression of Csde1-bound transcripts. Protein expression of ribogenesis factors Rpf2, Nop56 and Ebna1bp2 was reduced in the deletion mutant, while mRNA was unchanged. Protein expression of Pabpc1 was enhanced while Pabpc1 mRNA expression was reduced. Strikingly, the effect of reduced Csde1 function on mRNA stability and translation of Csde1-bound transcripts was modest. The correlation efficient between protein (iBAQ) and mRNA (RPKM) expression was not different between Csde1-bound and other transcripts. We suggest that Csde1 is involved in feed-back control in protein homeostasis and that it dampens oscillations in gene expression.

2018-10-24 | PXD006358 | Pride

Profiling of CSDE1-bound RNAs under MKRN2-mediated ubiquitination

Project description: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.

2026-02-02 | GSE317793 | GEO

Ribotag-RNA sequencing data using Csde1-KD dorsal root ganglion(DRG) neurons

Project description:We found that the expression of various ribosomal protein genes is regulated at the translation level, and the post-transcriptional regulator CSDE1 controls their association with ribosomes after sciatic nerve injury. This sequencing data shows neurons without CSDE1 exhibit a deficiency in the recruitment of ribosomal protein mRNAs to ribosomes.

2024-08-31 | GSE274619 | GEO

Co-immumnoprecipitation experiments to identify protein bindining partners of CSDE1

Project description:While the transcriptional network of human embryonic stem cells (hESCs) has been extensively studied, relatively little is known about how post-transcriptional modulations determine hESC function. RNA-binding proteins play central roles in RNA regulation, including translation and turnover. Here we show that the RNA-binding protein CSDE1 is highly expressed in hESCs to maintain their undifferentiated state and prevent default neural fate. Notably, loss of CSDE1 accelerates neural differentiation and potentiates neurogenesis. Conversely, ectopic expression of CSDE1 impairs neural differentiation. We find that CSDE1 post-transcriptionally modulates core components of multiple regulatory nodes of hESC identity, neuroectoderm commitment and neurogenesis. Among these key pro-neural/neuronal factors, CSDE1 binds fatty acid binding protein 7 (FABP7) and vimentin (VIM) mRNAs as well as transcripts involved in neuron projection development regulating their stability and translation. Thus, our results uncover CSDE1 as a central post-transcriptional regulator of hESC identity and neurogenesis. This proteomics dataset contains the data from co-immunopreciptation experiments using CSDE1 antibody in hESCs

2018-05-16 | PXD007271 | Pride

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

Unbiased identification of CSDE1-regulated targets during oncogene-induced senescence [polysome profiling]

2022-01-11 | GSE159998 | GEO