Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Discovery and functional interrogation of the virus and host RNA interactome of SARS-CoV-2 proteins [RNA-Seq]

ABSTRACT: Discovery and functional interrogation of the virus and host RNA interactome of SARS-CoV-2 proteins [RNA-Seq]

PROVIDER: PRJNA725867 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR14346737_1.fastq.gz	Fastqsanger.gz
	SRR14346737_2.fastq.gz	Fastqsanger.gz
	SRR14346738_1.fastq.gz	Fastqsanger.gz
	SRR14346738_2.fastq.gz	Fastqsanger.gz
	SRR14346739_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Discovery and functional interrogation of the virus and host RNA interactome of SARS-CoV-2 proteins

Project description:Discovery and functional interrogation of the virus and host RNA interactome of SARS-CoV-2 proteins

| PRJNA725849 | ENA

Discovery and functional interrogation of the virus and host RNA interactome of SARS-CoV-2 proteins [eCLIP]

Project description:Discovery and functional interrogation of the virus and host RNA interactome of SARS-CoV-2 proteins [eCLIP]

| PRJNA725841 | ENA

Discovery and functional interrogation of the virus and host RNA interactome of SARS-CoV-2 proteins [Ribo-Seq]

Project description:Discovery and functional interrogation of the virus and host RNA interactome of SARS-CoV-2 proteins [Ribo-Seq]

| PRJNA817264 | ENA

Discovery and functional interrogation of the virus and host RNA interactome of SARS-CoV-2 proteins [eCLIP]

Project description:The coronavirus disease 2019 (COVID-19) pandemic was caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). Understanding the molecular functions of SARS-CoV-2 proteins is thus imperative to developing effective antiviral treatments. Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral and host RNAs. SARS-CoV-2 proteins, NSP8 and NSP12, are found to specifically bind to untranslated regions of the RNA viral genome, with NSP12 additionally binding to all transcription regulatory sequences. This provides evidence for their central roles in replication and transcription. Moreover, we discovered a potential site of NSP12 mediated genome recombination, which could explain the genetic diversity found in coronaviruses. SARS-CoV-2 proteins exogenously expressed in human lung epithelial cells bind to 4,281 unique host RNAs. Nine SARS-CoV-2 proteins upregulate target gene expression, including NSP12 which upregulates mitochondrial electron transport and N-linked glycosylation proteins. Furthermore, siRNA knockdown of NSP12-targeted proteins in human lung organoid cells demonstrates substantial antiviral effects. Conversely, NSP9 inhibits host gene expression via blocking mRNA export and dampens antiviral inflammation response such as interleukin 1α (IL1α) production. Our extensive viral protein-RNA interactome provides a catalog of potential therapeutic targets and offers insight into the etiology of COVID-19 as a safeguard against future pandemics.

2022-03-09 | GSE173498 | GEO

Discovery and functional interrogation of the virus and host RNA interactome of SARS-CoV-2 proteins [RNA-Seq]

2022-03-09 | GSE173507 | GEO

Discovery and functional interrogation of the virus and host RNA interactome of SARS-CoV-2 proteins [Ribo-Seq]

2022-03-31 | GSE198899 | GEO

Discovery and functional interrogation of the virus and host RNA interactome of SARS-CoV-2 proteins

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-03-09 | GSE173508 | GEO

Systematic discovery and functional interrogation of SARS-CoV-2 viral RNA-host protein interactions during infection

Project description:Systematic discovery and functional interrogation of SARS-CoV-2 viral RNA-host protein interactions during infection

| PRJNA704334 | ENA

In silico discovery of the blood cell interactome

Project description:In silico discovery of the blood cell interactome

| PRJNA817538 | ENA

Characterization and functional interrogation of the SARS-CoV-2 RNA interactome.

Project description:Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic, which has led to a devastating global health crisis. The emergence of variants that escape neutralizing responses emphasizes the urgent need to deepen our understanding of SARS-CoV-2 biology. Using a comprehensive identification of RNA-binding proteins (RBPs) by mass spectrometry (ChIRP-MS) approach, we identify 107 high-confidence cellular factors that interact with the SARS-CoV-2 genome during infection. By systematically knocking down their expression in human lung epithelial cells, we find that the majority of the identified RBPs are SARS-CoV-2 proviral factors. In particular, we show that HNRNPA2B1, ILF3, QKI, and SFPQ interact with the SARS-CoV-2 genome and promote viral RNA amplification. Our study provides valuable resources for future investigations into the mechanisms of SARS-CoV-2 replication and the identification of host-centered antiviral therapies.

| S-EPMC9040432 | biostudies-literature

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