Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Direct and indirect consequences of PAB1 deletion in the regulation of translation initiation, translation termination, and mRNA decay [RNA-seq]

ABSTRACT: Cytoplasmic poly(A)-binding protein (PABPC, yeast Pab1) is involved in various stages of mRNA post-transcriptional control, including translation initiation, translation termination, and mRNA decay regulation. Due to the multi-functional properties of PABPC, attempts to define a specific role for PABPC in vivo by deleting, depleting, overexpressing, or mutating the protein has led to conflicting models of PABPC's function. To specifically assess direct and indirect consequences of deleting PABPC, we generated and analyzed RNA-Seq, ribosome profiling, and mass spectrometry data from yeast cells lacking Pab1.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE229691 | GEO | 2023/05/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Direct and indirect consequences of PAB1 deletion in the regulation of translation initiation, translation termination, and mRNA decay [Ribo-seq]

Project description:Cytoplasmic poly(A)-binding protein (PABPC, yeast Pab1) is involved in various stages of mRNA post-transcriptional control, including translation initiation, translation termination, and mRNA decay regulation. Due to the multi-functional properties of PABPC, attempts to define a specific role for PABPC in vivo by deleting, depleting, overexpressing, or mutating the protein has led to conflicting models of PABPC's function. To specifically assess direct and indirect consequences of deleting PABPC, we generated and analyzed RNA-Seq, ribosome profiling, and mass spectrometry data from yeast cells lacking Pab1.

2023-05-31 | GSE229692 | GEO

Direct and indirect consequences of PAB1 deletion in the regulation of translation initiation, translation termination, and mRNA decay

2023-06-09 | PXD041495 | Pride

Ribo-STAMP reveals translation status of RNAs bound by PABPN and PABPC

Project description:The poly(A) tail appended to the 3’ end of many eukaryotic transcripts plays a key role in the stability, nuclear transport, and translation of the RNA. These roles are largely mediated by the Poly(A) Binding Proteins (PABPs) that coat the poly(A) tails and interact with various proteins involved in the biogenesis and function of the RNA. While it is well established that the nuclear PABP (PABPN) binds newly synthesized poly(A) tails and is apparently replaced by the cytoplasmic PABP (PABPC) on transcripts exported to the cytoplasm, the distribution of transcripts for different genes or isoforms of the same gene on these distinct PABPs has not been investigated on a genome-wide scale. Here, we analyzed the identity, splicing status, poly(A) tail size, and translation status of RNAs co-immunoprecipitated with endogenous PABPN or PABPC in human cells. At steady state, many protein coding and non-coding RNAs exhibit strong bias for association with PABPN or PABPC. While PABPN-enriched transcripts more often were incompletely spliced and harbored longer poly(A) tails and PABPC-enriched RNAs tended to have longer half-lives and higher translation efficiency, there are curious outliers. Overall, our study reveals the landscape of RNAs bound by PABPN and PABPC, providing new details that support and advance the current understanding of the roles these proteins play in poly(A) tail synthesis, maintenance and function.

2022-03-30 | GSE195494 | GEO

Ribo-STAMP reveals translation status of RNAs bound by PABPN and PABPC

Project description:Ribo-STAMP reveals translation status of RNAs bound by PABPN and PABPC

| PRJNA800802 | ENA

The molecular basis of coupling between poly(A)-tail length and translational efficiency

Project description:In animal oocytes and early embryos, mRNA poly(A)-tail length strongly influences translational efficiency (TE), but later in development this coupling between tail length and TE disappears. Here, we elucidate how this coupling is first established and why it disappears. Overexpressing cytoplasmic poly(A)-binding protein (PABPC) in frog oocytes specifically improved translation of short-tailed mRNAs, thereby diminishing coupling between tail length and TE. Thus, coupling requires limiting PABPC, implying that in coupled systems longer-tail mRNAs better compete for limiting PABPC. In addition to expressing excess PABPC, post-embryonic cells had two other properties that prevented strong coupling: terminal-uridylation-dependent destabilization of mRNAs lacking bound PABPC, and a regulatory regime wherein PABPC contributes minimally to TE. Thus, these results revealed three fundamental mechanistic requirements for coupling and defined the context-dependent functions for PABPC, in which this protein promotes TE but not mRNA stability in coupled systems and mRNA stability but not TE in uncoupled systems.

2021-07-07 | GSE166544 | GEO

Cytoplasmic and nuclear fractionation from HEK293T cells

2022-03-30 | GSE195493 | GEO

Identification of different transcripts that favor the nuclear or cytoplasmic Poly(A) Binding Proteins (PABPs) through RNA immunoprecipitation

2022-03-30 | GSE195495 | GEO

The ribosomal protein Asc1/RACK1 is required for efficient translation of short mRNAs

Project description:Translation is a core cellular process carried out by a highly conserved macromolecular machine, the ribosome. There has been remarkable evolutionary adaptation of this machine through the addition of eukaryote-specific ribosomal proteins whose individual effects on ribosome function are largely unknown. Here we show that eukaryote-specific Asc1/RACK1 is required for efficient translation of mRNAs with short open reading frames that show greater than average translational efficiency in diverse eukaryotes. ASC1 mutants in S. cerevisiae display compromised translation of specific functional groups, including cytoplasmic and mitochondrial ribosomal proteins, and display cellular phenotypes consistent with their gene-specific translation defects. Asc1-sensitive mRNAs are preferentially associated with the translational ‘closed loop’ complex comprised of eIF4E, eIF4G and Pab1, and depletion of eIF4G mimics the translational defects of ASC1 mutants. Together our results reveal a role for Asc1/RACK1 in a length-dependent initiation mechanism optimized for efficient translation of genes with important housekeeping functions.

2016-04-24 | GSE61753 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of mRNA translation efficiency of Wild Type and Mettl3-/- mice

Project description:Considering m6A modification in mRNA was reported to be intensively corelated with RNA metabolism like RNA decay and RNA translation, we wonderd whether deleting Mettl3, the main catalzing enzyme, affect the RNA translation efficiency of mouse dendritic cells.

2019-04-02 | GSE108331 | GEO

RNAs associated with Upf1, Pab1, Rpl16a, Lsm1 proteins in yeast

Project description:Nonsense mediated mRNA decay (NMD) is a translation-dependent surveillance pathway that eliminates RNAs with short open reading frames (ORFs) and long 3' untranslated regions (UTRs). Upf1 is the key protein of this degradation pathway and we were interested to purify the associated RNAs. Moreover we have done purifications of two proteins from the general mRNA turnover in yeast : Pab1 and Lsm1 that both bind RNAs poly(A) tails. We have also done a purification with a protein from the small ribosomal subunit (40S) in order to have a look at the translated RNAs.

2022-10-01 | GSE160642 | GEO

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