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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

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			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

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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

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

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

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

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

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

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Ubiquitination of DEAD-box RNA helicase DDX3X by TRIM25

Project description:Tripartite motif protein 25 (TRIM25) is an E3 ligase that ubiquitinates multiple substrates within the RLR signalling cascade and plays both RING (really interesting new gene)-dependent and RING-independent roles in RIG-I-mediated IFN induction. We report that the PRY-SPRY domain of TRIM25 interacts with the N-terminal extension (NTE) of DEAD-box helicase 3X (DDX3X), a host protein with multiple roles in RLR signalling. Gene reporter assays and knockdown studies reveal DDX3X and TRIM25 cooperate to activate the IFN- promoter following RIG-I activation independent of DDX3X’s catalytic activity. We also show that TRIM25 ubiquitinates DDX3X at several lysine residues in vitro and in cells.

2021-09-08 | PXD028122 | Pride

A DEAD-box helicase drives the partitioning of a pro-differentiation NAB protein into nuclear foci

Project description:How cells regulate gene expression in a precise spatiotemporal manner during organismal development is a fundamental question in biology. Although the role of transcriptional condensates in gene regulation has been established, little is known about the function and regulation of these molecular assemblies in the context of animal development and physiology. Here we show that the evolutionarily conserved DEAD-box helicase DDX-23 controls cell fate in Caenorhabditis elegans by binding to and facilitating the condensation of MAB-10, the Caenorhabditis elegans homolog of mammalian NGFI-A-binding (NAB) protein. MAB-10 is a transcriptional cofactor that functions with the early growth response (EGR) protein LIN-29 to regulate the transcription of genes required for exiting the cell cycle, terminal differentiation, and the larval-to-adult transition. We suggest that DEAD-box helicase proteins function more generally during animal development to control the condensation of NAB proteins important in cell identity and that this mechanism is evolutionarily conserved. In mammals, such a mechanism might underlie terminal cell differentiation and when misregulated might promote cancerous growth.

2023-05-28 | GSE151399 | GEO

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