RRNA processing is surveilled by the mRNA guard protein Npl3
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1114745 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29131060_1.fastq.gz | Fastqsanger.gz | |||
| SRR29131060_2.fastq.gz | Fastqsanger.gz | |||
| SRR29131061_1.fastq.gz | Fastqsanger.gz | |||
| SRR29131061_2.fastq.gz | Fastqsanger.gz |
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Project description:Ribosomes mature stepwise on a long precursor-rRNA, the 35S rRNA in Saccharomyces cerevisiae. Successive cleavage and protein association generates the small and large subunits that join each other for translation. If the maturation encounters difficulties, pre-rRNA cleavage occurs irrevocably at site A3, generating the aberrant 23S rRNA that is degraded. We show that the mRNA guard protein Npl3 functions in rRNA maturation and its surveillance. In its absence, the early SSU processome assembly is disturbed as the ETS1 accumulates and some proteins are not loaded properly onto the rRNA. Additionally, the amount of the 23S rRNA increases, which indicates a novel role of Npl3 its removal. For this quality control function, Npl3 binds to the nascent pre-rRNA in a complex with the TRAMP-complex component Air1, but independently of Trf5. Although Trf5 is still able to mark such RNAs with an oligo d(T) sequence in npl3∆, this signal is not sufficient for full TRAMP complex assembly. Rather, the Npl3-mediated loading of Air1 supports the exosome recruitment and the elimination of the 23S rRNA. Thus, Npl3 represents a general RNA surveillance factor that clears the cell from faulty mRNA and rRNA products by recognition of processing defects and guiding degrading enzymes.
2025-05-01 | GSE268140 | GEO
Project description:SIRT7 is an NAD+-dependent protein deacetylase with important roles in ribosome biogenesis and cell proliferation. Previous studies have established that SIRT7 is associated with RNA polymerase I, interacts with pre-rRNA and promotes rRNA synthesis. Here we show that SIRT7 is also associated with snoRNAs that are involved in pre-rRNA processing and rRNA maturation. Knockdown of SIRT7 impairs U3 snoRNA-dependent early cleavage steps that are necessary for generation of 18S rRNA. Mechanistically, SIRT7 deacetylates U3-55k, a core component of the U3 snoRNP complex, and reversible acetylation of U3-55k modulates the association of U3-55k with U3 snoRNA. Deacetylation by SIRT7 enhances U3-55k binding to U3 snoRNA, which is a prerequisite for pre-rRNA processing. Under stress conditions, SIRT7 is released from nucleoli, leading to hyperacetylation of U3-55k and attenuation of prerRNA processing. The results reveal a multifaceted role of SIRT7 in ribosome biogenesis, regulating both transcription and processing of rRNA. CLIP-seq was performed in Flag-SIRT7-293T cells.
2016-01-07 | E-GEOD-76578 | biostudies-arrayexpress
Project description:SIRT7 is an NAD+-dependent protein deacetylase with important roles in ribosome biogenesis and cell proliferation. Previous studies have established that SIRT7 is associated with RNA polymerase I, interacts with pre-rRNA and promotes rRNA synthesis. Here we show that SIRT7 is also associated with snoRNAs that are involved in pre-rRNA processing and rRNA maturation. Knockdown of SIRT7 impairs U3 snoRNA-dependent early cleavage steps that are necessary for generation of 18S rRNA. Mechanistically, SIRT7 deacetylates U3-55k, a core component of the U3 snoRNP complex, and reversible acetylation of U3-55k modulates the association of U3-55k with U3 snoRNA. Deacetylation by SIRT7 enhances U3-55k binding to U3 snoRNA, which is a prerequisite for pre-rRNA processing. Under stress conditions, SIRT7 is released from nucleoli, leading to hyperacetylation of U3-55k and attenuation of prerRNA processing. The results reveal a multifaceted role of SIRT7 in ribosome biogenesis, regulating both transcription and processing of rRNA.
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Project description:Yeast Npl3 is a highly abundant RNA binding protein, related to metazoan SR proteins, with reported functions including transcription elongation, splicing and RNA 3’ end processing. To identify direct targets and functions for Npl3, we used UV crosslinking and analysis of cDNA (CRAC) to map precise RNA binding sites. Npl3 binds diverse RNA species, at sites indicative of roles in both early pre-mRNA processing and 3’ end formation on mRNAs and ncRNAs. Consistent with this, tiling array and RNAPII binding data revealed 3’ extended mRNA and snoRNA transcripts in the absence of Npl3. This reflected transcriptional readthrough by RNAPII, and extension and stabilization of cryptic unstable transcript (CUT) long noncoding RNAs. Transcription readthrough was widespread, often resulting in down-regulation of neighboring genes. We conclude that Npl3 is required for the formation of a termination-competent RNA, affecting both coding and noncoding RNAs.
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