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Perturbation of mRNP biogenesis reveals a dynamic landscape of the Rrp6-dependent surveillance machinery trafficking along the yeast genome (RNA-seq dataset)

ABSTRACT: Perturbation of mRNP biogenesis reveals a dynamic landscape of the Rrp6-dependent surveillance machinery trafficking along the yeast genome (RNA-seq dataset)

PROVIDER: PRJEB30458 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3013310.fastq.gz	Fastqsanger.gz
	ERR3013311.fastq.gz	Fastqsanger.gz
	ERR3013312.fastq.gz	Fastqsanger.gz
	ERR3013313.fastq.gz	Fastqsanger.gz
	ERR3013314.fastq.gz	Fastqsanger.gz

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Perturbation of mRNP biogenesis reveals a dynamic landscape of the Rrp6-dependent surveillance machinery trafficking along the yeast genome (RNA-seq dataset)

Project description:In order to dissect the nuclear RNA quality control (QC) mechanisms, we used a powerful assay based on global perturbation of mRNP biogenesis in yeast Saccharomyces cerevisiae by the bacterial Rho helicase. We have monitored the global RNA levels upon Rho activation and compare it to basal RNA level in WT strain, which have revealed down-regulated transcripts. Then, the same experiment was performed but in a strain lacking Rrp47, giving us a precise overview of the QC targets. We also followed some QC components (Nrd1, Nab3, Trf4 and Rrp6) along the yeast chromosomes by ChIP-seq before and after perturbation of mRNP biogenesis by Rho (crosslinked dataset).

2019-12-04 | E-MTAB-7538 | biostudies-arrayexpress

Perturbation of mRNP biogenesis reveals a dynamic landscape of the Rrp6-dependent surveillance machinery trafficking along the yeast genome (ChIP-seq dataset)

Project description:In order to dissect the nuclear RNA quality control (QC) mechanisms, we used a powerful assay based on global perturbation of mRNP biogenesis in yeast Saccharomyces cerevisiae by the bacterial Rho helicase. We have monitored the global RNA levels upon Rho activation and compare it to basal RNA level in WT strain, which have revealed down-regulated transcripts. Then, the same experiment was performed but in a strain lacking Rrp47, giving us a precise overview of the QC targets (crosslinked dataset). We also followed some QC components (Nrd1, Nab3, Trf4 and Rrp6) along the yeast chromosomes by ChIP-seq before (NI) and after (I) perturbation of mRNP biogenesis by Rho.

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Perturbation of mRNP biogenesis reveals a dynamic landscape of the Rrp6-dependent surveillance machinery trafficking along the yeast genome (ChIP-seq dataset)

Project description:Perturbation of mRNP biogenesis reveals a dynamic landscape of the Rrp6-dependent surveillance machinery trafficking along the yeast genome (ChIP-seq dataset)

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Perturbation of mRNP biogenesis reveals a dynamic landscape of the Rrp6-dependent surveillance machinery trafficking along the yeast genome.

Project description:Eukaryotic cells have evolved a nuclear quality control (QC) system to monitor the co-transcriptional mRNA processing and packaging reactions that lead to the formation of export-competent ribonucleoprotein particles (mRNPs). Aberrant mRNPs that fail to pass the QC steps are retained in the nucleus and eliminated by the exonuclease activity of Rrp6. It is still unclear how the surveillance system is precisely coordinated both physically and functionally with the transcription machinery to detect the faulty events that may arise at each step of transcript elongation and mRNP formation. To dissect the QC mechanism, we previously implemented a powerful assay based on global perturbation of mRNP biogenesis in yeast by the bacterial Rho helicase. By monitoring model genes, we have shown that the QC process is coordinated by Nrd1, a component of the NNS complex (Nrd1-Nab3-Sen1) involved in termination, processing and decay of ncRNAs which is recruited by the CTD of RNAP II. Here, we have extended our investigations by analyzing the QC behaviour over the whole yeast genome. We performed high-throughput RNA sequencing (RNA-seq) to survey a large collection of mRNPs whose biogenesis is affected by Rho action and which can be rescued upon Rrp6 depletion. This genome-wide perspective was extended by generating high-resolution binding landscapes (ChIP-seq) of QC components along the yeast chromosomes before and after perturbation of mRNP biogenesis. Our results show that perturbation of mRNP biogenesis redistributes the QC components over the genome with a significant hijacking of Nrd1 and Nab3 from genomic loci producing ncRNAs to Rho-affected protein-coding genes, triggering termination and processing defects of ncRNAs.

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Tho2 participates in yeast nuclear mRNP quality control by recruiting the 3'-5' exoribonuclease Rrp6

Project description:In order to dissect the nuclear RNA quality control (QC) mechanisms, we used a powerful assay based on global perturbation of mRNP biogenesis in yeast Saccharomyces cerevisiae by the bacterial Rho helicase. We have monitored the recruitment of THO complex subunit upon Rho activation, which revealed that Tho2 was over-recruited in opposition to its counterparts. We then tracked the recruitment of Rrp6 upon Rho induction in WT strain and in strains lacking either Mft1 or Tho2, showing the implication of Tho2 in Rrp6 recruitment over Rho induction. Finally, we measured the recruitment of Rrp6 upon partial deletion of Tho2 C-terminal domain responsible for its RNA interaction ability, proving that Tho2 presence on the chromatin is required for the Rho-induced Rrp6 recruitment..

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Tho2 participates in yeast nuclear mRNP quality control by recruiting the 3'-5' exoribonuclease Rrp6

Project description:Tho2 participates in yeast nuclear mRNP quality control by recruiting the 3'-5' exoribonuclease Rrp6

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rrp6 delta and rrp6 delta, trf4 delta vs WT

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2005-04-28 | GSE2579 | GEO

ChIP-chip analyses of H3K9 methylation in rrp6 deletion and rrp6 alp13 double mutant S.pombe cells.

Project description:ChIP-chip analyses of H3K9 methylation in rrp6 deletion (exosome mutant) and in rrp6 alp13 double mutant S.pombe cells. Keywords: ChIP-chip

2007-04-23 | GSE7136 | GEO

Transcriptome-wide view of endosomal mRNP transport [iCLIP ]

Project description:Spatiotemporal protein expression is mediated by active transport and local translation of mRNAs. Key factors of the transport machinery are RNA-binding proteins (RBPs) that recognise mRNAs as cargo for motor-based transport. However, a global view of transported mRNAs with cognate RBP binding sites is missing. Here, we cast a transcriptome-wide view on endosomal mRNP transport in Ustilago maydis by studying the newly identified endosomal RBP Grp1 and the key transport RBP Rrm4 in a comparative iCLIP approach. This uncovered thousand of cargo mRNAs bound by both RBPs.

2018-12-10 | GSE109557 | GEO

Transcriptome-wide view of endosomal mRNP transport [RNA-Seq]

2018-12-10 | GSE109560 | GEO