Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq analysis of control and NRDE2-depleted breast cancer cells

ABSTRACT: Purpose: investigate transcriptomic changes following depletion of the NRDE2 gene Methods: MDA-MB-231 breast cancer cells were transfected with 20nM control or NRDE2-targeting siRNAs, and RNA was collected after 48h for RNA-seq analysis Results: We analyzed si-Control and si-NRDE2-treated samples in triplicate (~46-64 million reads per sample) and find that the near-complete loss of NRDE2 results in generally modest changes in gene expression, with only 84 genes deregulated >2-fold. We also identify 342 introns which are differentially retained in NRDE2-depleted cells. Conclusions: NRDE2 is required for suppressing intron retention in a subset of genes

ORGANISM(S): Homo sapiens

PROVIDER: GSE119827 | GEO | 2018/09/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

NRDE2 negatively regulates nuclear exosome functions II

Project description:To examine whether NRDE2 can impact the competition between hMTR4 and ALYREF, we performed stranded RNA-seq to detect nuclear RNAs isolated from NRDE2 and control knockdown cells.

2019-03-14 | GSE120203 | GEO

NRDE2 negatively regulates nuclear exosome functions I

Project description:To examine whether NRDE2 can impact the competition between hMTR4 and ALYREF, we performed stranded RNA-seq to detect total RNAs isolated from NRDE2 and control knockdown cells.

2019-03-14 | GSE120202 | GEO

NRDE2 negatively regulates nuclear exosome functions IV

Project description:To examine whether NRDE2 can impact the competition between hMTR4 and ALYREF, we performed stranded RNA-seq to detect RNAs isolated from MTR4 IP in NRDE2 and control knockdown cells.

2019-03-14 | GSE120205 | GEO

NRDE2 negatively regulates nuclear exosome functions

Project description:The exosome functions in the degradation of diverse RNA species, yet how it is negatively regulated remains largely unknown. Here, we show that NRDE2 forms a 1:1 complex with MTR4, a nuclear exosome cofactor critical for exosome recruitment, via a conserved MTR4-interacting domain (MID). Unexpectedly, NRDE2 mainly localizes in nuclear speckles, where it inhibits MTR4 recruitment and RNA degradation, and thereby ensures efficient mRNA nuclear export. Structural and biochemical data revealed that NRDE2 interacts with MTR4's key residues, locks MTR4 in a closed conformation, and inhibits MTR4 interaction with the exosome as well as proteins important for MTR4 recruitment, such as the cap-binding complex (CBC) and ZFC3H1. Functionally, MID deletion results in the loss of self-renewal of mouse embryonic stem cells. Together, our data pinpoint NRDE2 as a nuclear exosome negative regulator that ensures mRNA stability and nuclear export.

2019-03-14 | GSE120206 | GEO

NRDE2 negatively regulates nuclear exosome functions

Project description:NRDE2 negatively regulates nuclear exosome functions

| PRJNA491937 | ENA

RNA-seq analysis of control and NRDE2-depleted breast cancer cells

Project description:RNA-seq analysis of control and NRDE2-depleted breast cancer cells

| PRJNA490376 | ENA

NRDE2 negatively regulates nuclear exosome functions I

Project description:NRDE2 negatively regulates nuclear exosome functions I

| PRJNA491944 | ENA

NRDE2 negatively regulates nuclear exosome functions II

Project description:NRDE2 negatively regulates nuclear exosome functions II

| PRJNA491941 | ENA

NRDE2 negatively regulates nuclear exosome functions IV

Project description:NRDE2 negatively regulates nuclear exosome functions IV

| PRJNA491939 | ENA

Novel RNA-binding Proteins Bind U1 snRNA to Promote Splicing of Weak 5' Splice Sites

Project description:Removal of introns during pre-mRNA splicing, which is central to gene expression, initiates by base pairing of U1 snRNA with a 5' splice site (5'SS). In mammals, many introns contain weak 5'SSs that are not efficiently recognized by the canonical U1 snRNP, suggesting alternative mechanisms exist. Here, we develop a cross-linking immunoprecipitation coupled to a high-throughput sequencing method, BCLIP-seq, to identify NRDE2 (Nuclear RNAi defective-2) and CCDC174 (Coiled-Coil Domain-Containing 174) as novel RNA-binding proteins in mouse ES cells that associate with U1 snRNA and unspliced 5'SSs. Both proteins bind directly to U1 snRNA independently of canonical U1 snRNP specific proteins, and they are required for the selection and effective processing of weak 5'SSs. Our results reveal that mammalian cells use non-canonical splicing factors bound directly to U1 snRNA to effectively select suboptimal 5'SS sequences in hundreds of genes, promoting proper splice site choice and accurate pre-mRNA splicing.

2023-09-07 | PXD029392 | Pride

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