Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

In vivo atlas of RNA secondary structures recognized by ADARs [RNA-Seq]

ABSTRACT: We performed irCLASH and HiCLIP for ADAR1-3 in HEK293 cells. In addition, we performed mRNA-seq in ADAR1-3 overexpressed HEK293 cells and control HEK293 cells

ORGANISM(S): Homo sapiens

PROVIDER: GSE136326 | GEO | 2020/03/26

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

In vivo atlas of RNA secondary structures recognized by ADARs [irCLASH-seq&hiCLIP-seq]

Project description:We performed irCLASH and HiCLIP for ADAR1-3 in HEK293 cells. In addition, we performed mRNA-seq in ADAR1-3 overexpressed HEK293 cells and control HEK293 cells

2020-03-26 | GSE136325 | GEO

In vivo atlas of RNA secondary structures recognized by ADARs

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

2020-03-25 | GSE136327 | GEO

In vivo atlas of RNA secondary structures recognized by ADARs

Project description:In vivo atlas of RNA secondary structures recognized by ADARs

| PRJNA562274 | ENA

In vivo atlas of RNA secondary structures recognized by ADARs [RNA-Seq]

Project description:In vivo atlas of RNA secondary structures recognized by ADARs [RNA-Seq]

| PRJNA562385 | ENA

In vivo atlas of RNA secondary structures recognized by ADARs [irCLASH-seq&hiCLIP-seq]

Project description:In vivo atlas of RNA secondary structures recognized by ADARs [irCLASH-seq&hiCLIP-seq]

| PRJNA562384 | ENA

hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1.

Project description:The structure of messenger RNA is important for post-transcriptional regulation, mainly because it affects binding of trans-acting factors. However, little is known about the in vivo structure of full-length mRNAs. Here we present hiCLIP, a biochemical technique for transcriptome-wide identification of RNA secondary structures interacting with RNA-binding proteins (RBPs). Using this technique to investigate RNA structures bound by Staufen 1 (STAU1) in human cells, we uncover a dominance of intra-molecular RNA duplexes, a depletion of duplexes from coding regions of highly translated mRNAs, an unexpected prevalence of long-range duplexes in 3' untranslated regions (UTRs), and a decreased incidence of single nucleotide polymorphisms in duplex-forming regions. We also discover a duplex spanning 858 nucleotides in the 3' UTR of the X-box binding protein 1 (XBP1) mRNA that regulates its cytoplasmic splicing and stability. Our study reveals the fundamental role of mRNA secondary structures in gene expression and introduces hiCLIP as a widely applicable method for discovering new, especially long-range, RNA duplexes.

| S-EPMC4376666 | biostudies-literature

How do ADARs bind RNA? New protein-RNA structures illuminate substrate recognition by the RNA editing ADARs.

Project description:Deamination of adenosine in RNA to form inosine has wide ranging consequences on RNA function including amino acid substitution to give proteins not encoded in the genome. What determines which adenosines in an mRNA are subject to this modification reaction? The answer lies in an understanding of the mechanism and substrate recognition properties of adenosine deaminases that act on RNA (ADARs). Our recent publication of X-ray crystal structures of the human ADAR2 deaminase domain bound to RNA editing substrates shed considerable light on how the catalytic domains of these enzymes bind RNA and promote adenosine deamination. Here we review in detail the deaminase domain-RNA contact surfaces and present models of how full length ADARs, bearing double stranded RNA-binding domains (dsRBDs) and deaminase domains, could process naturally occurring substrate RNAs.

| S-EPMC5501306 | biostudies-literature

RNA sequencing quantitative analysis of RNA editing levels in ADAR1, ADAR2, AIMP2 overexpression and wild type HEK293 cells

Project description:We overexpressed ADAR1, ADAR2 and AIMP2 in HEK293 cells and examined editing using RNA-seq.

2017-10-01 | GSE87198 | GEO

2022_de Reuver_ADAR1 +/+ vs ADAR1 Za/Za HEK293 cells (deep-seq)

Project description:ADAR1 +/+ vs ADAR1 Za/Za HEK293 cells (deep-seq)

| PRJEB52618 | ENA

ADAR1-mediated RNA editing promotes B cell lymphomagenesis.

Project description:The project aims to evaluate the contribution of ADAR1 RNA editing to B cell lymphomagenesis, specifically in diffuse large B cell lymphoma (DLBCL). Within our DLBCL cohort, RNA editing targets transcripts within known lymphoma-driving pathways such as apoptosis, p53 and NF-kB signaling, as well as the previously unrecognized RIG-I-like pathway. In the latter context, we show that ADAR1-mediated editing in the MAVS transcript correlates with increased MAVS protein expression levels, associating with increased interferon/NF-kB signaling and increased T cell exhaustion. To confirm this mechanism, we have performed LC-MSMS analysis on a DLBCL cell line (RCK8) in the presence or absence of ADAR1 (Figure S11D ). Additionally, using targeted RNA base editing tools to restore editing within MAVS 3'UTR in ADAR1-deficient cells, we demonstrate that editing is likely to be causal to an increase in downstream signaling in the absence of activation by canonical nucleic acid receptor sensing. To confirm that this signaling increase depends on an increase of MAVS protein upon specific editing, we have performed LC-MSMS analysis on the same samples (Figure 4G).

2023-07-20 | PXD041549 | 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