Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Xrn1 activates transcription, translation and decay of mRNAs encoding membrane proteins

ABSTRACT: To study the role of the exonuclease Xrn1 in translational control, we performed ribosome profiling and RNA-seq in Xrn1-depleted cells. By using an auxin-inducible degron, we were able to study immediate effects of Xrn1 depletion in translational control. Therefore, we could overcome experimental limitations associated to stable deletion mutants.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE109734 | GEO | 2019/02/08

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Xrn1 modulates the dynamic osmostress response at a transcriptional and translational level

Project description:To study the role of the exonuclease Xrn1 in gene expression dynamics under osmotic stress conditions, we performed RNA-seq in Xrn1-depleted cells. By using an auxin-inducible degron, we were able to study immediate effects of Xrn1 depletion in gene expression dynamics. Therefore, we could overcome experimental limitations associated to stable deletion mutants.

2023-01-28 | GSE144440 | GEO

Xrn1 activates transcription, translation and decay of mRNAs encoding membrane proteins

Project description:Xrn1 activates transcription, translation and decay of mRNAs encoding membrane proteins

| PRJNA431807 | ENA

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.

2011-11-08 | E-MEXP-27 | biostudies-arrayexpress

The exonuclease Xrn1 activates transcription and translation of mRNAs encoding membrane proteins.

Project description: Not available

| S-EPMC6428865 | biostudies-literature

Transcriptomic analysis of the Xrn1 depletion by Auxin-degron shutoff

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.

2019-02-22 | GSE123326 | GEO

Xrn1 biochemically associates to the eisosome after the post diauxic shift in yeast

Project description:mRNA degradation is one of the main steps of gene expression, and a key player is the 5’-3’ exonuclease Xrn1. In Saccharomyces cerevisiae, it was previously shown, by a microscopy approach, that Xrn1 is located to different cellular compartments, depending on physiological state. During exponential growth, Xrn1 is distributed in the cytoplasm, while it is present in the eisosomes after the post-diauxic shift (PDS). Here, we biochemically characterized the Xrn1-associated complexes in different cellular states. We demonstrate that, after PDS, Xrn1 but not the decapping (DCP), nor Lsm1-7/Pat1 complexes, was sequestered in the eisosomes, thus preserving mRNAs from degradation.

2023-09-15 | PXD044514 | Pride

Xrn1 biochemically associates to the eisosome after the post diauxic shift in yeast (3)

2023-09-15 | PXD044634 | Pride

Xrn1 biochemically associates to the eisosome after the post diauxic shift in yeast (2)

2023-09-15 | PXD044631 | Pride

Xrn1 biochemically associates to the eisosome after the post diauxic shift in yeast (4)

2023-09-15 | PXD044653 | Pride

RNA-controlled nucleocytoplasmic shuttling of mRNA decay factors regulates mRNA synthesis and a novel mRNA decay pathway

Project description:mRNA level is controlled by factors that mediate both mRNA synthesis and decay, including the 5’ to 3’ exonuclease Xrn1 - a major mRNA synthesis and decay factor. Here we show that nucleocytoplasmic shuttling of several mRNA decay factors plays a key role in determining both mRNA synthesis and decay. Shuttling is regulated by RNA-controlled binding of the karyopherin Kap120 to two nuclear localization sequences (NLSs) in Xrn1, location of one of which is conserved from yeast to human. The decaying RNA binds and masks NLS1, establishing a link between mRNA decay and Xrn1 shuttling. Preventing Xrn1 import, either by deleting KAP120 or mutating the two Xrn1 NLSs, compromise transcription and, unexpectedly, also the cytoplasmic decay, uncovering a cytoplasmic decay pathway that initiates in the nucleus. Most mRNAs are degraded by both the “classical” and the novel pathways, the ratio between them represents a full spectrum. Importantly, Xrn1 shuttling is required for proper adaptation to environmental changes, in particular to ever changing environmental fluctuations.

2022-09-19 | PXD036414 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data