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Schizosaccharomyces pombe

ABSTRACT: The conserved protein Seb1 from fission yeast is recruited to the chromatin during active Pol II transcription

PROVIDER: PRJNA360641 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5168400.fastq.gz	Fastqsanger.gz
	SRR5168401.fastq.gz	Fastqsanger.gz
	SRR5168402.fastq.gz	Fastqsanger.gz
	SRR5168395.fastq.gz	Fastqsanger.gz
	SRR5168396.fastq.gz	Fastqsanger.gz

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The conserved protein Seb1 from fission yeast is recruited to the chromatin during active Pol II transcription

Project description:The protein Seb1 from fission yeast contains a conserved CTD-interacting domain (CID) with which it can bind to phosphorylated forms of the Pol II C-terminal domain (CTD) during active transcription. It mainly interacts with Ser2P-CTD but also with Ser5P-CTD. Here, we show the recruitment profile of the protein to chromatin using ChIP-Seq which is mediated mainly via binding to the Pol II-CTD. In addition, it can also interact with nascent RNA via its RNA recognition motif (RRM) domain.

2017-02-14 | GSE93342 | GEO

Comparison of RNA profiling between wild type, med20∆, rrp6∆ and med20∆/rrp6∆ in Schizosaccharomyces pombe

Project description:Mediator is a co-regulator of RNA polymerase II (Pol II), transducing signals from regulatory elements and transcription factors to the general transcription machinery at the promoter. We here demonstrate that Med20 influences ribosomal protein expression in fission yeast. In addition, loss of Med20 leads to an accumulation of aberrant readthrough tRNA transcripts. The aberrant transcripts are polyadenylated and targeted for degradation by the exosome. Similarly, other specialized RNA molecules, such as snRNA, snoRNA and rRNA are also accumulated in the absence of Med20. We suggest that fission yeast Mediator takes part in a regulatory pathway of Pol III transcripts.

2016-01-01 | GSE73792 | GEO

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Project description:Cohesin localisation along fission yeast chromosomes delineates conserved mechanisms of binding

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Project description:RNA pol II transcript abundance controls condensin accumulation at mitotically upregulated and heat shock-inducible genes in fission yeast

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Schizosaccharomyces pombe

Project description:The conserved protein Seb1 drives transcription termination by binding RNA polymerase II and nascent RNA

| PRJNA354266 | ENA

Comparison of RNA profiling between wild type, med20â, rrp6â and med20â/rrp6â in Schizosaccharomyces pombe

Project description:Mediator is a co-regulator of RNA polymerase II (Pol II), transducing signals from regulatory elements and transcription factors to the general transcription machinery at the promoter. We here demonstrate that Med20 influences ribosomal protein expression in fission yeast. In addition, loss of Med20 leads to an accumulation of aberrant readthrough tRNA transcripts. The aberrant transcripts are polyadenylated and targeted for degradation by the exosome. Â Similarly, other specialized RNA molecules, such as snRNA, snoRNA and rRNA are also accumulated in the absence of Med20. We suggest that fission yeast Mediator takes part in a regulatory pathway of Pol III transcripts. RNA-sequencing of wt, med20â, rrp6â, med20â/rrp6â strains using wt as control. Each strain was sequenced using three biological replicas. The results were analyzed for differential expression.

2016-07-03 | E-GEOD-73792 | biostudies-arrayexpress

The conserved protein Seb1 drives transcription termination by binding RNA polymerase II and nascent RNA

Project description:Termination of Pol II transcription is an important step in the transcription cycle and is responsible for dislodgement of polymerase from DNA which leads to the release of a functional transcript. Recent studies have identified key players important for termination and showed a conserved domain that interacts with the phosphorylated C-terminus of Pol II (CTD-Interacting-Domain, CID) to constitute a common feature of these proteins. However, the mechanism by which transcription termination is achieved, is not understood. Using genome-wide methods, we demonstrate that the fission yeast CID protein Seb1 is essential for termination of protein-coding and non-coding genes through interacting with S2-phosphorylated Pol II and nascent RNA. Furthermore, we present the crystal structures of the Seb1 CTD- and RNA-binding modules. Unexpectedly, the latter reveals a novel intertwined two-domain arrangement of a canonical RRM and a second domain. These results provide important insights into the mechanism underlying eukaryotic transcription termination.

2017-02-05 | GSE89914 | GEO

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Project description:Transcription profile of fission yeast

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Seb1 proximity dependent biotinylation (PDB) in Schizosaccharomyces pombe

Project description:Transcription by RNA polymerase I (RNAPI) represents most of the transcriptional activity in eukaryotic cells and is associated with the production of mature ribosomal RNA (rRNA). As several rRNA maturation steps are coupled to RNAPI transcription, the rate of RNAPI elongation directly influences processing of nascent pre-rRNA, and changes in RNAPI transcription rate can result in alternative rRNA processing pathways in response to growth conditions and stress. However, factors and mechanisms that control RNAPI progression by influencing transcription elongation rate remain poorly understood. Our project is to show that the conserved RNA-binding Seb1 is a pausing-promoting factor for RNA polymerases I to control cotranscriptional RNA processing. Here, we did a proximity dependent biotinylation followed by mass spectrometry (PDB-MS) of the Seb1 protein in order to assess for physical interactions with the RNAPI transcription machinery. A mutant E. coli BirA enzyme is fused to the Seb1 protein. This mutant version of BirA uses biotin to catalyze the formation of biotinoyl-5′-AMP (bioAMP), thereby generating a ‘cloud’ of activated biotin molecules that can react with free primary amines (most often lysine residues) of neighboring proteins. This experiment will support the conclusion that Seb1 is located at the rDNA locus.

2023-05-02 | PXD037768 | Pride

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Project description:Fission yeast, an excellent model organism.

| PRJNA9517 | ENA