DEAD-box ATPase Dbp2 mediates mRNA release after 3’-end formation
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ABSTRACT:
PROVIDER: PRJEB71979 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR12511913.fastq.gz | Fastqsanger.gz | |||
| ERR12511914.fastq.gz | Fastqsanger.gz | |||
| ERR12511915.fastq.gz | Fastqsanger.gz | |||
| ERR12511916.fastq.gz | Fastqsanger.gz | |||
| ERR12511917.fastq.gz | Fastqsanger.gz |
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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
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 RNA-seq, we determined RNA expression profiles of a conditional depletion strain of Dbp2 and the corresponding wild type. For this, we placed the endogenous dbp2 gene under the control of the P.nmt1 promoter, which is repressed in the presence of thiamine. Cells were harvested at the beginning (t0) or the end (t5 or t9) of shift to thiamine-containing YES medium. S. cerevisiae spike-in cells were added in a 1:5 OD600 ratio immediately before harvesting.
2024-06-30 | E-MTAB-13717 | biostudies-arrayexpress
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 calibrated RNAPII-ChIP-seq, we determined the transcription profiles of a conditional depletion strain of Dbp2 and the corresponding wild type. For this, we placed the endogenous dbp2 gene under the control of the P.nmt1 promoter, which is repressed in the presence of thiamine. Cells were crosslinked at the beginning (t0) or the end (t9) of a 9h shift to thiamine-containing YES medium. S. cerevisiae spike-in cells were added in a 1:5 OD600 ratio immediately before crosslinking.
2024-06-30 | E-MTAB-13714 | biostudies-arrayexpress
Project description:mRNA biogenesis in the eukaryotic nucleus is a highly complex process. The numerous RNA processing steps are spatially and temporally coordinated to ensure that only fully processed transcripts are released into the nucleoplasm for export from the nucleus. Here, we explore the hypothesis that fission yeast Dbp2, a ribonucleoprotein complex (RNP) remodelling ATPase of the DEAD-box family, is involved in a RNP assembly checkpoint at the 3’-end of genes that is coupled to the release of the 3’-end processing complex after polyadenylation. We show that Dbp2 interacts with the cleavage and polyadenylation complex (CPAC) and localizes to cleavage bodies, which are enriched for 3’-end processing factors and proteins involved in nuclear RNA surveillance. Upon loss of Dbp2, 3’-processed, polyadenylated RNAs accumulate on chromatin and in cleavage bodies, which is accompanied by a depletion of CPAC components from the soluble pool. Under these conditions, cells display an increased likelihood to skip polyadenylation sites as well as delayed transcription termination, suggesting that the availability of CPAC components is insufficient to maintain normal levels of 3’-end processing. Our data is consistent with a model in which Dbp2 is involved in an mRNP remodelling checkpoint that licenses RNA export and is coupled to CPAC release.
2024-07-04 | PXD048560 | Pride
Project description:DEAD-box ATPase Dbp2 mediates mRNA release after 3’-end formation - III
| PRJEB71965 | ENA
Project description:DEAD-box ATPase Dbp2 mediates mRNA release after 3’-end formation - II
| PRJEB71980 | ENA
Project description:Accurate gene expression requires the coordination of RNA processing with assembly of messenger RNA-protein (mRNP) complex. RNA helicases are a class of enzymes that unwind RNA duplexes in vitro and have been are proposed to remodel RNA structure in vivo. Herein, we provide evidence that the DEAD-box protein Dbp2 remodels RNA structure to facilitate efficient pre-mRNA processing in S. cerevisiae. First, we find that Dbp2 associates with the 3’ ends and 3’ splice-sites of mRNAs genome-wide. Using structure-seq to map RNA secondary structure, we find altered secondary structures in dbp2∆ cells that overlap polyadenylation elements and correlate with inefficient termination. We also identify a role for Dbp2 in pre-mRNA splicing and show that both splicing and termination require Dbp2 helicase activity. This reveals that DEAD-box RNA helicases unwind structure in vivo and that structural alteration of pre-mRNA is essential for proper gene expression.
2019-05-01 | GSE106478 | GEO
Project description:Accurate gene expression requires the coordination of RNA processing with assembly of messenger RNA-protein (mRNP) complex. RNA helicases are a class of enzymes that unwind RNA duplexes in vitro and have been are proposed to remodel RNA structure in vivo. Herein, we provide evidence that the DEAD-box protein Dbp2 remodels RNA structure to facilitate efficient pre-mRNA processing in S. cerevisiae. First, we find that Dbp2 associates with the 3’ ends and 3’ splice-sites of mRNAs genome-wide. Using structure-seq to map RNA secondary structure, we find altered secondary structures in dbp2∆ cells that overlap polyadenylation elements and correlate with inefficient termination. We also identify a role for Dbp2 in pre-mRNA splicing and show that both splicing and termination require Dbp2 helicase activity. This reveals that DEAD-box RNA helicases unwind structure in vivo and that structural alteration of pre-mRNA is essential for proper gene expression.
2019-05-01 | GSE106477 | GEO
Project description:Proper formation of messenger RNA-protein complexes (mRNPs) is critical for accurate gene expression and requires temporal regulation of mRNA structures. RNA helicases are major players that control mRNP/mRNA structures throughout the life of mRNAs. Our group has shown that the DEAD-box RNA helicase Dbp2 in S. cerevisiae is a bona fide RNA helicase in vitro that is required for proper transcription termination and assembly of RNA-binding proteins onto poly(A)+ RNA in vivo. Here, we utilized multiple genome-wide approaches to identify the mRNAs and processing steps targeted by the enzymatic activity of Dbp2. We found that Dbp2 promotes efficient termination of mRNA transcription through remodeling of RNA structures at the 3’ end of mRNAs. This finding elucidates how an RNA helicase regulates gene expression by modulating RNA structures at a genome-wide scale. In addition, Dbp2 facilitates efficient splicing, for which the helicase activity of Dbp2 is required. This reveals a previously uncharacterized role of RNA helicases besides known splicing factors. Overall, our work shows that Dbp2 plays a critical role in pre-mRNA processing and how RNA structure remodeling impacts gene expression.
2019-05-01 | GSE125283 | GEO
Project description:DEAD-box RNA helicases are ATP-dependent RNA binding proteins and RNA-dependent ATPases that possess weak, nonprocessive unwinding activity in vitro, but they can form long-lived complexes on RNAs when the ATPase activity is inhibited. Ded1 is a yeast DEAD-box protein, the functional ortholog of mammalian DDX3, that is considered important for the scanning efficiency of the 48S pre-initiation complex ribosomes to the AUG start codon. We used a modified PAR-CLIP technique, which we call quicktime PAR-CLIP (qtPAR-CLIP) to crosslink Ded1 to 4-thiouridine-incorported RNAs in vivo using UV light centered at 365 nm. The irradiation conditions are largely benign to the yeast cells and to Ded1, and we are able to obtain a high efficiency of crosslinking under physiological conditions. We find that Ded1 forms crosslinks on the open reading frames of many different mRNAs, but it forms the most extensive interactions on a relatively few mRNAs, and particularly on mRNAs encoding certain ribosomal proteins and translation factors. Under glucose-depletion conditions the crosslinking pattern shifts to mRNAs encoding metabolic and stress-related proteins, which reflects the altered translation. These data are consistent with Ded1 functioning in the regulation of translation elongation, perhaps by pausing or stabilizing the ribosomes through its ATP-dependent binding.
2023-08-01 | GSE228828 | GEO