Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The DEAD-box protein Dbp2p is linked to non-coding RNAs, the helicase Sen1p, and R-loops

ABSTRACT: The DEAD-box protein Dbp2p is linked to non-coding RNAs, the helicase Sen1p, and R-loops

PROVIDER: PRJNA451258 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7051270.fastq.gz	Fastqsanger.gz
	SRR7051271.fastq.gz	Fastqsanger.gz
	SRR7051272.fastq.gz	Fastqsanger.gz
	SRR7051273.fastq.gz	Fastqsanger.gz
	SRR7051274.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

The DEAD-box protein Dbp2p is linked to non-coding RNAs, the helicase Sen1p, and R-loops [iCLIP]

Project description:The DEAD-box RNA helicase Dbp2p is highly conserved in eukaryotes and has been implicated in transcription, ribosome biogenesis, mRNP assembly, nuclear export, and lncRNA function. How Dbp2p functions in these seemingly unrelated biological roles is not known. An important step towards addressing this question is the determination of cellular RNA binding sites of Dbp2p. Here, we identify transcriptome-wide RNA binding sites of Dbp2p from Saccharomyces cerevisiae using denaturing tandem affinity purification followed by UV-crosslinking. We find that Dbp2p crosslinks to mRNAs and ribosomal RNAs, and most markedly to non-coding RNAs, including snoRNA, snRNAs, and tRNAs. In snoRNAs, Dbp2p preferentially interacts with sites near the 3’ ends. These sites closely correspond to regions where RNA-DNA hybrids (R-loop) form, and to binding sites of the RNA helicase Sen1p, a component of the Nrd1-Nab3-Sen1 (NNS) complex, which functions in transcription termination and 3' processing of non-coding RNAs in yeast. We also show that Dbp2p interacts in an RNA-independent manner with Sen1p in vivo. We further observe Dbp2p crosslinks to tRNAs and other RNAs also at sites where RNA-loops form. Collectively, our data link Dbp2p to diverse non-coding RNAs, to Sen1p, and to R-loops. The transcriptome-wide connection to R-loops provides a unifying theme for seemingly unrelated cellular roles of Dbp2p.

2018-04-22 | GSE113488 | GEO

The DEAD-box protein Dbp2p is linked to non-coding RNAs, the helicase Sen1p, and R-loops [iCLIP]

Project description:The DEAD-box protein Dbp2p is linked to non-coding RNAs, the helicase Sen1p, and R-loops [iCLIP]

| PRJNA451261 | ENA

The DEAD-box protein Dbp2p is linked to non-coding RNAs, the helicase Sen1p, and R-loops [RNA-Seq]

2018-04-22 | GSE113487 | GEO

The DEAD-box protein Dbp2p is linked to non-coding RNAs, the helicase Sen1p, and R-loops [RNA-Seq]

Project description:The DEAD-box protein Dbp2p is linked to non-coding RNAs, the helicase Sen1p, and R-loops [RNA-Seq]

| PRJNA451260 | ENA

Dual roles of DEAD-box RNA helicase Brr2 in genome stability

Project description:R-loop is a common chromatin feature consisting of a displaced single-stranded DNA and an RNA-DNA hybrid, and dysregulation of R-loop surveillance results in genomic and transcriptomic instability. Although the RNA moiety of most R-loops originates from linear transcripts, circular RNAs (circRNAs), outputs from back-splicing, can also hybridize with the complementary strand of a DNA duplex. However, how circRNA-associated R-loops (ciR-loops) are monitored remains elusive. Here, we identified the DEAD-box RNA helicase Brr2 as an evolutionarily-conserved ciR-loop repressor with dual roles in inhibiting circRNA generation and resolving harmful ciR-loops. Accumulation of ciR-loops caused by loss-of-function of this dual-action factor induces antisense transcription and premature transcription termination for many genes and generates significant DNA damage, which further leads to a series of defects in DNA replication, cell division and cell proliferation. We propose that functional integration of multilayered regulation by a single protein can be an efficient double protection against genome instability.

2025-08-11 | GSE279102 | GEO

DEAD-box ATPase Dbp2 mediates mRNA release after 3’-end formation

Project description:DEAD-box ATPases belong to an abundant class of proteins that are involved in virtually all aspects of RNA metabolism and are found in all kingdoms of life. When bound to a DEAD-box ATPase, the RNA substrate is forced into a kinked conformation that is incompatible with helical structures. Distortion of the RNA can result in unwinding of short RNA duplexes (helicase activity) or destabilize RNA-protein interactions, allowing DEAD-box ATPases to remodel mRNPs (RNPase activity). The RNPase activity makes DEAD-box ATPases suitable molecular building blocks for the implementation of checkpoints that confer directionality to the process of RNA biogenesis. Here, we provide data that characterizes the DEAD-box ATPase Dbp2 (SPBP8B7.16c) of the fission yeast Schizosaccharomyces pombe. Using ChIP-seq, we determined the sites where HTP-tagged Dbp2 associates with chromatin. ChIP-seq of Srp2-HTP is included as a reference protein that is known to associate with transcribing RNA polymerase II (RNAPII).

2024-06-30 | E-MTAB-13712 | biostudies-arrayexpress

Dual roles of DEAD-box RNA helicase Brr2 in genome stability

Project description:Dual roles of DEAD-box RNA helicase Brr2 in genome stability

| PRJNA1170866 | ENA

The DEAD-box RNA helicase Ded1 is a translation-elongation factor

Project description:The DEAD-box RNA helicase Ded1 is a translation-elongation factor

| PRJNA951699 | ENA

Organ-differential Regulation of Vascular Development by DEAD-box Helicase 24

Project description:Organ-differential Regulation of Vascular Development by DEAD-box Helicase 24

| PRJNA768417 | ENA

Discriminating activities of DEAD-Box Helicase 41 from myeloid malignancy-associated germline variants by genetic rescue

Project description:Although DEAD-box helicase 41 (DDX41) is implicated in oncogenic and innate immune mechanisms, there are many unanswered questions about how the ever-increasing spectrum of genetic variants impacts DDX41 activity. Here, we describe a facile genetic rescue assay that discriminates activities of DDX41 from those of human myeloid malignancy-linked germline and somatic DDX41 mutants. Our analyses revealed that the variants were impaired in their intrinsic RNA-regulatory activities and to induce monocytic differentiation markers. It will be instructive to extend these analyses to more broadly conduct structure/function assessments for clinical genetic curation and leverage the quantitative assay to elucidate mechanisms and interventions that promote and/or oppose DDX41 function, thereby influencing DDX41-linked pathogenicity.

2022-12-04 | GSE208400 | 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