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CRAC of yeast RNA polymerase II in the absence or upon depletion of Xrn1

ABSTRACT: CRAC of yeast RNA polymerase II in the absence or upon depletion of Xrn1

PROVIDER: PRJNA641389 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12075764.fastq.gz	Fastqsanger.gz
	SRR12075765.fastq.gz	Fastqsanger.gz
	SRR12075766.fastq.gz	Fastqsanger.gz
	SRR12075767.fastq.gz	Fastqsanger.gz
	SRR12075768.fastq.gz	Fastqsanger.gz

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CRAC of yeast RNA polymerase II in the absence or upon depletion of Xrn1

Project description:We report RNA polymerase II occupancy profiles across the genome of S.cerevisiae strains deleted or depleted for the protein Xrn1. This allowed investigating the role of Xrn1 in RNA polymerase II transcription.

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Transcription profiling of yeast wild type, xrn1, xrn1 upf1, xrn1 nmd2, and xrn1 upf3 strains to investigate mRNA decay

Project description:To determine the effects of inactivation of both the nosense-mediated mRNA decay pathway and the general 5' to 3' decay pathway on yeast mRNA decay, we compared the expression profiles of the wild-type, xrn1, xrn1 upf1, xrn1 nmd2, and xrn1 upf3 strains.

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CRAC of yeast RNA polymerase II in Topoisomerase 1 and 2 depleted cells

Project description:We obtained RNA polymerase II profiles across the genome of S.cerevisiae cells harbouring Top1-AID and Top2-AID tagged proteins. Cells were treated with anauxin analog (IAA) to induce degradation of Top1-AID and Top2-AID. This allowed us to compare RNAPII in absence of Top1 and Top2 activity to the control condition (absence of IAA treatment).

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CRAC of yeast RNA polymerase II in anchor-away and auxin-degron strains.

Project description:CRAC of yeast RNA polymerase II in anchor-away and auxin-degron strains.

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CRAC of yeast RNA polymerase II in Topoisomerase 1 and 2 depleted cells

Project description:CRAC of yeast RNA polymerase II in Topoisomerase 1 and 2 depleted cells

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Xrn1 influence on gene transcription results from the combination of general effects on elongating RNA pol II and gene-specific chromatin configuration [Mnase-seq]

Project description:mRNA homeostasis is favored by crosstalk between transcription and degradation machineries. Both the Ccr4-Not and the Xrn1-decaysome complexes have been described to influence transcription. While Ccr4-Not has been shown to directly stimulate transcription elongation, the information available on how Xrn1 influences transcription is scarce and contradictory. In this study we have addressed this issue by mapping RNA polymerase II (RNA pol II) at high resolution, using CRAC and BioGRO-seq techniques in Saccharomyces cerevisiae. We found significant effects of Xrn1 perturbation on RNA pol II profiles across the genome. RNA pol II profiles at 5’ exhibited significant reductions in slope that were compatible with decreased elongation rates. This phenomenon was also observed soon after the nuclear pool of Xrn1 was depleted. Nucleosome mapping confirmed drastically altered chromatin dynamics. We also found an accumulation of arrested RNA pol II at the 3’ end, immediately upstream of polyadenylation sites of most genes, with particular incidence in those functionally related to regulatory processes. Lack of Xrn1 provoked alterations in RNA pol II CTD phosphorylation and increased recruitment of 3’ pre-mRNA processing factors. However, accumulation of RNA pol II at 3’ ends was rather related to the nucleosomal configuration of those regions.

2021-05-24 | GSE153035 | GEO

Xrn1 influence on gene transcription results from the combination of general effects on elongating RNA pol II and gene-specific chromatin configuration [RNA-seq]

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Transcriptomic analysis of mutant yeast strains deficient in Xrn1 nuclear import

Project description:The goal of the project was to study the transcription rates and mRNA levels, genome-wide, in several mutants in Xrn1 defetive in nuclear import. We used Genomic Run-On (GRO) experiment in wild type and xrn1 mutant strains.

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Total RNA-Seq in wild-type (WT), dcr1, xrn1 and xrn1 dcr1 strains of N. castellii

Project description:Antisense (as)lncRNAs are extensively degraded by the nuclear exosome and the cytoplasmic exoribonuclease Xrn1 in the budding yeast Saccharomyces cerevisiae, lacking RNA interference (RNAi). Whether the ribonuclease III Dicer affects aslncRNAs in close RNAi-capable relatives remains unknown. Using genome-wide RNA profiling, here we show that aslncRNAs are primarily targeted by the exosome and Xrn1 in the RNAi-capable budding yeast Naumovozyma castellii, Dicer only affecting Xrn1-sensitive lncRNAs (XUTs) levels in Xrn1-deficient cells. The dcr1 and xrn1 mutants display synergic growth defects, indicating that Dicer becomes critical in absence of Xrn1. Small RNA sequencing showed that Dicer processes aslncRNAs into small RNAs, with a preference for asXUTs. Consistently, Dicer localizes into the cytoplasm. Finally, we observed an expansion of the exosome-sensitive antisense transcriptome in N. castellii compared to S. cerevisiae, suggesting that the presence of cytoplasmic RNAi has reinforced the nuclear RNA surveillance machinery to temper aslncRNAs expression. Our data provide fundamental insights into aslncRNAs metabolism and open perspectives into the possible evolutionary contribution of RNAi in shaping the aslncRNAs transcriptome.

2019-08-21 | GSE90041 | GEO

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Project description:The goal of the project was to study the effects on transcription and mRNA stability of the Xrn1 sudden depletion. We analyzed the effect of Xrn1 depletion caused by protein degradation of an Auxin-degron fusion on the transcription rates, mRNA stabilities and mRNA levels by doing Genomic Run-On (GRO) experiments at 30 min after Auxin addition with a control at 0 min.

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