Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-sequencing of PC3M prostate cancer cells depleted of the RNA binding protein HNRNPA2B1

ABSTRACT: RNA-sequencing of PC3M prostate cancer cells depleted of the RNA binding protein HNRNPA2B1

PROVIDER: PRJNA814296 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR18283047_1.fastq.gz	Fastqsanger.gz
	SRR18283047_2.fastq.gz	Fastqsanger.gz
	SRR18283048_1.fastq.gz	Fastqsanger.gz
	SRR18283048_2.fastq.gz	Fastqsanger.gz
	SRR18283049_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

RNA-sequencing of PC3M prostate cancer cells depleted of the RNA binding protein HNRNPA2B1

Project description:RNA binding proteins (RBPs) play important roles in cellular stress responses. Here we investigated the association between HNRNPA2B1, an RBP upregulated in prostate cancer, and expression of genes in stress response pathways. HNRNPA2B1 depletion in vitro using siRNA resulted in altered expression of multiple genes in the unfolded protein response (UPR) pathway in PC3M prostate cancer cells.

2025-03-08 | GSE198261 | GEO

The RNA binding protein HNRNPA2B1 regulates RNA abundance and motor protein activity in neurites

Project description:RNA molecules are localized to subcellular regions through interactions between localization-regulatory cis-elements and trans-acting RNA binding proteins (RBPs). However, the identities of RNAs whose localization is regulated by a specific RBP as well as the impacts of that RNA localization on cell function have generally remained unknown. Here, we demonstrate that the RBP HNRNPA2B1 acts to keep specific RNAs out of neuronal projections. Using subcellular fractionation, high-throughput sequencing, and single molecule RNA FISH, we find that hundreds of RNAs demonstrate markedly increased abundance in neurites in HNRNPA2B1 knockout cells. These RNAs often encode motor proteins and are enriched for known HNRNPA2B1 binding sites and motifs in their 3′ UTRs. The speed and processivity of microtubule-based transport is impaired in these cells, specifically in their neurites. HNRNPA2B1 point mutations that increase its cytoplasmic abundance relative to wildtype lead to stronger suppression of both RNA mislocalization and transport defects than seen with wildtype HNRNPA2B1. We further find that the subcellular localizations of HNRNPA2B1 target RNAs are sensitive to perturbations of RNA decay machinery, suggesting that it is HNRNPA2B1’s known role in regulating RNA stability that may explain these observations. These findings establish HNRNPA2B1 as a negative regulator of neurite RNA abundance and link the subcellular activities of motor proteins with the subcellular abundance of the RNAs that encode them.

2024-08-20 | GSE275212 | GEO

The RNA binding protein HNRNPA2B1 regulates IFNG signaling in macrophages

Project description:Heterogeneous nuclear ribonucleoprotein A2B1 (HNRNPA2B1) is a well known RNA binding protein but the mechanisms by which it contributes to innate immune gene regulation is poorly understood. Here we report that HNRNPA2B1 functions in macrophages to regulate IFNG signaling through alternative splicing of the IFNG receptor. Specific deletion of HNRNPA2B1 in macrophages using our newly developed conditional mice crossed to LysMCre resulted in altered cytokine responses in both an endotoxic shock model and following Salmonella infection. Interestingly, while HNRNPA2B1 can function as a viability gene, we observed increased macrophage and neutrophil numbers in the KO mice following LPS induced endotoxic shock. HNRNPA2B1 KO mice were more susceptible to Salmonella and Mycobacterium Tuberculosis infections and failed to effectively clear the pathogens. Mechanistically, loss of HNRNPA2B1 resulted in an increase in No-GO transcripts of the IFNG receptor (Ifngr) leading to lower expression of the receptor at the cell surface impacting the downstream IFNG signaling cascade. Collectively, our data highlights an important role for HNRNPA2B1 in regulating IFNG signaling in macrophages.

2024-09-30 | GSE243269 | GEO

Nuclear HNRNPA2B1 HITS-CLIP and RNA-seq

Project description:To identify HNRNPA2B1 binding sites on endogenous nuclear RNAs, we performed HITS-CLIP for endogenous HNRNPA2B1 and RNA-seq to analyze the nuclear RNA under either METTL3 or HNRNPA2B1 depletion. Wild type MDA-MB-231 cells were subjected to the HITS-CLIP procedure on immunoprecipitated HNRNPA2B1 associated RNA obtained from the nuclear fraction (Licatalosi D, et al. 2008, Nature 456:464-U22). For RNA-seq, nuclear RNA was extracted from MDA-MB-231 or Hela cells knocked down for METTL3 or HNRNPA2B1.

2015-06-20 | E-GEOD-70061 | biostudies-arrayexpress

The RNA binding protein HNRNPA2B1 regulates IFNG signaling in macrophages

Project description:The RNA binding protein HNRNPA2B1 regulates IFNG signaling in macrophages

| PRJNA1017506 | ENA

Nuclear HNRNPA2B1 HITS-CLIP and RNA-seq

2015-06-20 | GSE70061 | GEO

SMALL MOLECULE INHIBITORS OF HNRNPA2B1-RNA INTERACTIONS REVEAL A PREDICTABLE SORTING OF RNA SUBSETS INTO EXTRACELLULAR VESICLES

Project description:Extracellular vesicles (EVs) are cell-secreted membranous particles contributing to intercellular communication. Coding and non-coding RNAs are widely detected as EV cargo, and RNAbinding proteins (RBPs), such as hnRNPA2B1, have been circumstantially implicated in EV-RNA sorting mechanisms. However, the contribution of competitive RBP-RNA interactions responsible for RNA-sorting outcomes is still unclear, especially for predicting the EV-RNA content. We designed a reverse proteomic analysis exploiting the EV-RNA to identify intracellular protein binders in vitro and used cells expressing a recombinant hnRNPA2B1 to normalize competitive interactions. Interestingly, we prioritized heterogeneous nuclear ribonucleoproteins in networks including RAB proteins and recognizing purine-rich RNA sequences representing a subset of previously identified EXO motifs. A screening campaign using a full-length human hnRNPA2B1 protein and a synthetic purine-rich RNA probe brought to small molecule inhibitors orthogonally validated through biochemical and cell-based approaches. Selected drugs effectively interfered with a post-transcriptional layer impacting secreted EV-RNAs, reducing the vesicular pro-inflammatory miR-221 while counteracting the hnRNPA2B1- or TDP43Q331K-dependent paracrine activation of NF-kB in EV recipient cells. These results demonstrate the relevance of post-transcriptional mechanisms for EV-RNA sorting and the possibility of predicting the EV-RNA quality for developing innovative strategies targeting discrete paracrine functions.

2025-02-24 | PXD052658 | Pride

The RNA binding protein HNRNPA2B1 regulates RNA abundance and motor protein activity in neurites

Project description:The RNA binding protein HNRNPA2B1 regulates RNA abundance and motor protein activity in neurites

| PRJNA1149810 | ENA

Sumoylated hnrnpa2b1 controls the sorting of miRNAs into two exosomes through binding to specific motifs

Project description:Exosomes are released by most cells to the extracellular environment, and are involved in cell-to-cell-communication. Exosomes contain specific repertoires of mRNAs, miRNAs and other non-coding RNAs that can be functionally transferred to recipient cells. However, the mechanisms that control the specific loading of RNA species into exosomes remain unknown. Here we describe short sequence motifs present in miRNAs that control their localization into exosomes. The protein hnRNPA2B1 specifically binds exosomal miRNAs through the recognition of these motifs and controls their loading into exosomes. Moreover, hnRNPA2B1 in exosomes is sumoylated, and sumoylation controls the binding of hnRNPA2B1 to miRNAs. The loading of miRNAs into exosomes can be modulated by mutagenesis of the identified motifs or changes in hnRNPA2B1 expression levels. These findings identify hnRNPA2B1 as a key player in miRNA sorting into exosomes and provide potential tools for the packaging of selected regulatory RNAs into exosomes and their use in biomedical applications.

2014-04-16 | PXD000350 | Pride

Prostate Cancer and Normal Adjacent Prostate RNA-seq samples, NGS-ProToCol

Project description:The dataset "Prostate Cancer and Normal Adjacent Prostate RNA-seq samples, NGS-ProToCol" includes 41 Normal Adjacent Prostate and 51 ribo-depleted Prostate Cancer RNA-seq samples.

| EGAS00001002816 | EGA

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