Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SARS-CoV-2 -1 PRF RNA Pull Down and SFL Pull Down

ABSTRACT: To identify the protein partners of SARS-CoV-2 -1 PRF RNA, we performed RNA pull-down assays using streptavidin magnetic beads. To obtain more accurate and reliable data, tRSA sequence-tagged -1 PRF and -1 FSE RNA probes were both used to capture binding proteins in our screen. As a random sequence control for nonspecificity, the equivalent proteins extracted from H1299 cells were incubated with tRSA-labeled -1 PRF and -1 FSE RNA probes. A high-throughput technology, LC/MS-MS(MS), was applied to identify the candidate interacting proteins of SARS-CoV-2 -1 PRF RNA.

ORGANISM(S): Homo Sapiens

SUBMITTER: Xiaozhong Peng

PROVIDER: PXD042504 | iProX | Thu May 25 00:00:00 BST 2023

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Similar Datasets

Capturing SARS-cov in low abundant patient samples: a comparative analysis (arbo double ms) .

Project description:In this study, we tested the efficacy of five commercial probes panels at detecting SARS-CoV-2 genome including panels from Illumina, Twist Bioscience and Arbor Bioscience. To do so, we used 19 patient nasal swab samples broken down into 5 series of 4 samples of equivalent SARS-CoV-2 viral load (cycle threshold (CT): low CT means a high viral load – CT26, CT29, CT32, CT35 and CT36+).

2022-06-01 | E-MTAB-11232 | biostudies-arrayexpress

Capturing SARS-cov in low abundant patient samples: a comparative analysis (arbo single MS).

2022-06-01 | E-MTAB-11235 | biostudies-arrayexpress

Capturing SARS-cov in low abundant patient samples: a comparative analysis (Twist sarscov MS).

2022-06-01 | E-MTAB-11234 | biostudies-arrayexpress

Capturing SARS-cov in low abundant patient samples: a comparative analysis (Illumina respv NS).

2022-02-08 | E-MTAB-11233 | biostudies-arrayexpress

Capturing SARS-cov in low abundant patient samples: a comparative analysis (metagenomics NS).

2022-06-01 | E-MTAB-11236 | biostudies-arrayexpress

Capturing SARS-cov in low abundant patient samples: a comparative analysis (twist panviral NS).

2022-06-01 | E-MTAB-11237 | biostudies-arrayexpress

The short isoform of the host antiviral protein ZAP acts as an inhibitor of SARS-CoV-2 programmed ribosomal frameshifting

Project description:Programmed ribosomal frameshifting (PRF) is a fundamental gene expression event in many viruses, including SARS-CoV-2. It allows production of essential viral structural and replicative enzymes that are encoded in an alternative reading frame. Despite the importance of PRF for the viral life cycle, it is still largely unknown how and to what extent cellular factors alter mechanical properties of frameshift elements and thereby impact virulence. This prompted us to comprehensively dissect the interplay between the SARS-CoV-2 frameshift element and the host proteome. We reveal that the short isoform of the zinc-finger antiviral protein (ZAP-S) is a direct regulator of PRF in SARS-CoV-2 infected cells. ZAP-S overexpression strongly impairs frameshifting and inhibits viral replication. Using in vitro ensemble and single-molecule techniques, we further demonstrate that ZAP-S directly interacts with the SARS-CoV-2 RNA and interferes with the folding of the frameshift RNA element. Together, these data identify ZAP-S as a host-encoded inhibitor of SARS-CoV-2 frameshifting and expand our understanding of RNA-based gene regulation.

2021-11-25 | PXD029656 | Pride

Genome-wide CRISPR screens identify noncanonical translation factor eIF2A as an enhancer of SARS-CoV-2 programmed –1 ribosomal frameshifting

Project description:Many positive-strand RNA viruses, including all known coronaviruses, employ programmed –1 ribosomal frameshifting (–1 PRF) to regulate the translation of polycistronic viral RNAs. However, only a few host factors have been shown to regulate –1 PRF. Through a reporter-based genome-wide CRISPR/Cas9 knockout screen, we identified several host factors that either suppressed or enhanced –1 PRF of SARS-CoV-2. One of these factors is eukaryotic translation initiation factor 2A (eIF2A), which specifically and directly enhanced –1 PRF in vitro and in cells. Consistent with the crucial role of efficient –1 PRF in transcriptase/replicase expression, loss of eIF2A reduced SARS-CoV-2 replication in cells. Transcriptome-wide analysis of eIF2A-interacting RNAs showed that eIF2A primarily interacted with 18S ribosomal RNA near the contacts between the SARS-CoV-2 frameshift-stimulatory element (FSE) and the ribosome. Thus, our results revealed an unexpected role for eIF2A in modulating the translation of specific RNAs independent of its previously described role during initiation.

2024-07-11 | GSE223690 | GEO

SARS-CoV-2 FSE RNA pull down combined with LC-MS/MS analysis

Project description:To identify potential cellular RNA-binding proteins (RBPs) that interact with the FSE RNA of SARS-CoV-2, biotinylated in vitro transcription (IVT) FSE RNA from the SARS-CoV-2 genome was incubated with lysates of H460 cells infected with human coronavirus OC43 (HCoV-OC43) and Huh7 cells infected with human coronavirus 229E (HCoV-229E). To exclude non-specific binders, a non-related RNA was used as a control.

2026-04-07 | PXD076663 |

Mouse hippocampus RNA pull down LC-MS/MS

Project description:Antisense and sense probes of noncoding RNA GAS5 were used to perform the RNA pull down experiment on mouse hippocampus tissues. Then the proteins were identified by LC-MS/MS.

2021-09-09 | PXD023363 | 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