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Saccharomyces cerevisiae BY4741

ABSTRACT: The Ski complex binds 80S ribosomes for 3’ to 5’ decay of mRNA

PROVIDER: PRJNA288089 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2078180.fastq.gz	Fastqsanger.gz
	SRR2078181.fastq.gz	Fastqsanger.gz
	SRR2078182.fastq.gz	Fastqsanger.gz
	SRR2078183.fastq.gz	Fastqsanger.gz

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The Ski complex binds 80S ribosomes for 3’ to 5’ decay of mRNA

Project description:Cytoplasmic degradation of eukaryotic mRNAs in 3’ to 5’ direction is catalyzed by the exosome complex together with the Ski complex and, in the yeast Saccharomyces cerevisiae, the Ski7 protein. This exosome-Ski-system also degrades ribosome-associated aberrant mRNAs lacking a stop codon, a pathway called non-stop-mRNA decay (NSD). However, the interplay between the Ski components and the ribosome is unknown. Here, we report that the Ski complex can associate with ribosomes in vitro and in vivo independently of Ski7. Ribosome profiling suggests that this association is important for NSD but also for general mRNA turnover. A cryo-electron microscopy structure reveals that the Ski complex binds near the mRNA entry site of the 40S subunit, facilitating the threading of the mRNA into the Ski2 helicase. Collectively, these results demonstrate an unanticipated role for the Ski complex in mRNA decay of ribosome-associated mRNAs, mediated by a direct interaction with the translation machinery.

2017-02-10 | GSE70259 | GEO

Saccharomyces cerevisiae BY4741

Project description:Quality control of transcription start site selection by Nonsense-Mediated-mRNA Decay

| PRJNA270241 | ENA

Human SKI component SKIV2L regulates telomeric DNA-RNA hybrids and prevents telomere fragility

Project description:Super killer (SKI) complex is a well-known cytoplasmic 3′ to 5′ mRNA decay complex that functions with the exosome to degrade excessive and aberrant mRNAs. Recently, SKIV2L, the 3′ to 5′ RNA helicase of the human SKI (hSKI) complex has been implicated with the extraction of mRNA at stalled ribosomes, tackling aberrant translation. Here, we show that SKIV2L and TTC37 of the hSKI complex are present within the nucleus, localise on chromatin and at some telomeres during the G2 cell cycle phase. In cells, SKIV2L prevents telomere replication stress shown as fragile telomeres and increases the stability of telomere DNA-RNA hybrids in G2 of the cell cycle whereas its absence decreases the amount of those structures. We further demonstrate that purified hSKI complex binds telomeric DNA and RNA substrates in vitro. Moreover, SKIV2L association with telomeres is dependent on DNA-RNA hybrids but its helicase activity is dispensable for its telomeric function. Taken together, our results provide a nuclear function for SKIV2L of the hSKI complex in overcoming replication stress at telomeres mediated by its recruitment to DNA-RNA hybrid structures in G2 and thus maintaining telomere stability.

2024-10-03 | PXD046955 | Pride

Saccharomyces cerevisiae

Project description:mRNA decay data set

| PRJNA91935 | ENA

The ASC-1 complex promotes translation initiation of the scanning ribosomes

Project description:Translation is initiated by binding of the eIF4F complex to the 5' cap of the mRNA, which is followed by scanning of the initiation codon by scanning ribosomes. Here we demonstrate that the ASC-1 complex (ASCC), which was previously shown to promote the dissociation of colliding 80S ribosomes, associates with the scanning ribosomes to regulate translation initiation. Sel-TCP-seq analysis revealed that ASCC3, a subunit of ASCC with a helicase domain, localizes predominantly to the 5' untranslated region of mRNAs. Knockdown of ASCC3 resulted in reduced translation efficiency associated with reduced 43S preinitiation complex (PIC) loading and a reduced speed of scanning ribosomes. In addition, depletion of the ubiquitin ligase ZNF598, a sensor of collided 80S ribosomes, also reduces the PIC loading and speed of scanning ribosomes. Our results have thus revealed that ASCC is required not only for dissociation of colliding 80S ribosomes, but also for efficient translation initiation by scanning ribosomes.

2023-03-31 | GSE186502 | GEO

Saccharomyces cerevisiae BY4741

Project description:Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex

| PRJNA377523 | ENA

Saccharomyces cerevisiae BY4741

Project description:Transcriptome maps of mRNP biogenesis factors define pre-mRNA recognition

| PRJNA245894 | ENA

Saccharomyces cerevisiae BY4741

Project description:Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains

| PRJNA271405 | ENA

Saccharomyces cerevisiae

Project description:Heritable variation of mRNA decay rates in yeast

| PRJNA258654 | ENA

LARP1 senses free ribosomes to coordinate supply and demand of ribosomal proteins

Project description:Terminal oligopyrimidine motif-containing (TOP) mRNAs encode all ribosomal proteins in mammals and are regulated to tune ribosome synthesis to cell state. Previous studies implicate LARP1 in 40S- or 80S-ribosome complexes that repress and stabilize TOP mRNAs. However, a mechanistic understanding of how LARP1 and TOP mRNAs interact with ribosomes to coordinate TOP mRNA outcomes is lacking. Here, we show that LARP1 senses the cellular supply of ribosomes by directly binding non-translating 80S ribosomes. Cryo-EM structures reveal a previously uncharacterized domain of LARP1 bound to and occluding the 40S mRNA channel and mutations at the LARP1-ribosome interface block formation of the 40S/80S-LARP1-TOP complexes. Free cytosolic ribosomes induce sequestration of TOP mRNAs in repressed 80S-LARP1-TOP complexes independent of alterations in mTOR signaling. Together, this work demonstrates a ribosome-sensing function of LARP1 that allows it to tune ribosome protein synthesis to the availability of free ribosomes.

2023-10-28 | GSE246077 | GEO

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