Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Lariat mapping of wild type and DBR1 KO cells after knockdown of AQR

ABSTRACT: Lariat mapping of wild type and DBR1 KO cells after knockdown of AQR

PROVIDER: PRJNA801683 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR17809365_1.fastq.gz	Fastqsanger.gz
	SRR17809365_2.fastq.gz	Fastqsanger.gz
	SRR17809366_1.fastq.gz	Fastqsanger.gz
	SRR17809366_2.fastq.gz	Fastqsanger.gz
	SRR17809367_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 48

Similar Datasets

Lariat mapping of DBR1 KO and DBR1 KO+DBR1 addback cells

Project description:We constructed a DBR1 knockout cell line (C22) using CRISPR in HEK293T cells. Through mapping of lariat reads, lariat levels in the DBR1 - samples are shown to increase dramatically (~20x) relative to wild type cells. Over 60% of this increase in lariat levels is abrogated upon rescue of DBR1 - cells with a DBR1 expression vector

2022-01-29 | GSE195469 | GEO

Lariat mapping of wild type and DBR1 KO cells after knockdown of AQR

Project description:Using wild type HEK293T cells and our DBR1 CRISPR knockout cell line (C22), we investigated the effect of AQR knockdown on cellular lariat levels. Samples were taken after transfection with either one of two AQR-targeting siRNAs or a non-targeting control siRNA. After sequencing the samples, lariat mapping of the reads revealed that AQR knockdown increased the lariat recovery rate by ~50% relative to the level observed in the negative control samples.

2022-01-31 | GSE195668 | GEO

Lariat mapping of DBR1 KO and DBR1 KO+DBR1 addback cells

Project description:Lariat mapping of DBR1 KO and DBR1 KO+DBR1 addback cells

| PRJNA800759 | ENA

Lariat mapping of a DBR1 CRISPR KO cell line

Project description:We used CRISPR in HEK293T cells to create two DBR1 knockout cell lines (C19 and C22). After high-throughput sequencing of total RNA extracted from these cells, we performed lariat read mapping using the method described in "Large-scale mapping of branchpoints in human pre-mRNA transcripts in vivo" (Taggart et al, 2012). We found lariats in the two DBR1- cell lines to be ~20-fold enriched relative to the levels observed in the HEK293T control samples.

2022-02-03 | GSE195586 | GEO

Lariat mapping of a DBR1 CRISPR KO cell line

Project description:Lariat mapping of a DBR1 CRISPR KO cell line

| PRJNA801289 | ENA

Debranching enzyme DBR1-mediated lariat RNA turnover requires ALBA proteins in Arabidopsis

Project description:Lariat RNAs, generated as by-products of RNA splicing from excised introns, must be removed. RNA debranching enzyme (DBR1) is the core factor responsible for lariat RNA removal. However, the mechanism by which DBR1 debranches lariat RNAs remains unclear. Here, we demonstrate that six ALBA (Acetylation Lowers Binding Affinity) proteins interact with DBR1 to enhance its debranching activity and facilitate DBR1's accessibility to lariat RNAs, thereby promoting lariat RNA turnover. Similar to dbr1, alba mutants exhibit pleiotropic developmental defects and accumulate lariat RNAs. ALBAs bind to lariat RNAs via their C-terminal RGG/RG-rich repeats and assist DBR1 in binding to these RNAs. The N-terminal ALBA domain mediates the interaction with DBR1 and enhances its enzymatic activity. Cold stress induces lariat RNA accumulation by attenuating the ALBA–DBR1 interaction, which in turn reduces the induction of cold-responsive genes by impairing their transcription. Together, these findings uncover that lariat RNA turnover requires ALBA proteins.

2025-11-20 | GSE284756 | GEO

The Debranching Enzyme Dbr1 Regulates Lariat Turnover and Intron Splicing

Project description:The majority of genic transcription is intronic. Introns are removed by splicing as branched lariat RNAs which require rapid recycling. The branch site is recognized during splicing catalysis and later debranched by Dbr1 in the rate-limiting step of lariat turnover. Through generation of the first viable DBR1 knockout cell line, we find the predominantly nuclear Dbr1 enzyme to encode the sole debranching activity in human cells. Dbr1 preferentially debranches substrates that contain canonical U2 binding motifs, suggesting that branchsites discovered through sequencing do not necessarily represent those favored by the spliceosome. We find that Dbr1 also exhibits specificity for particular 5' splice site sequences. We identify Dbr1 interactors through co-immunoprecipitation mass spectroscopy. We present a mechanistic model for Dbr1 recruitment to the branchpoint through the intron-binding protein AQR. In addition to a 20-fold increase in lariats, Dbr1 depletion increases exon skipping. Using ADAR fusions to timestamp lariats, we demonstrate a defect in spliceosome recycling. In the absence of Dbr1, spliceosomal components remain associated with the lariat for a longer period of time. As splicing is co-transcriptional, slower recycling increases the likelihood that downstream exons will be available for exon skipping.

2023-06-26 | MSV000092263 | MassIVE

DBR1 Interactors Identification Analysis in TTDN1 KO background

Project description:DBR1 interactors were identified from HeLa-S cells (WT or TTDN1 KO).

2024-08-09 | PXD042563 | Pride

Debranching enzyme DBR1-mediated lariat RNA turnover requires ALBA proteins in Arabidopsis

Project description:Debranching enzyme DBR1-mediated lariat RNA turnover requires ALBA proteins in Arabidopsis

| PRJNA1200608 | ENA

A comprehensive map of intron branchpoints and lariat RNAs in plants

Project description:Lariat is formed by excised intron, in which the 5' splice site joints with the branchpoint (BP) during splicing. Although lariat RNAs are usually degraded by DBR1 (RNA debranching enzyme 1), recent findings in animals showed that many lariat RNAs were widely detected under physiological conditions. In contrast, the features of BPs and to what extent lariat RNAs accumulate naturally are largely unexplored in plants. Here, we analyzed 948 RNA sequencing datasets to document plant BPs and lariat RNAs on a genome-wide scale. In total, we identified 13872, 5199, 29582, and 13478 BPs in Arabidopsis, tomato, rice, and maize, respectively. Features of plant BPs are highly similar to those in yeast and human, in that BPs are adenine-preferred and flanked by uracil-enriched sequences. Intriguingly, ~20% of introns harbor multiple BPs, and BP usage is tissue-specific. Furthermore, 10580 lariat RNAs accumulate in wild type Arabidopsis plants, and most of these lariat RNAs originate from longer or retroelement-depleted introns, and the expression of these lariat RNAs significantly correlated with the incidence of back-splicing of parent exons. Collectively, our results provide the first comprehensive map of intron BPs and lariat RNAs in plants, and uncover a novel link between lariat turnover and splicing.

2019-04-17 | GSE117416 | GEO

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