Crac analysis of the Bud22 ribosome biogenesis factor
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ABSTRACT:
PROVIDER: PRJNA884356 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21710710.fastq.gz | Fastqsanger.gz | |||
| SRR21710711.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: Pre-ribosomal RNA is cleaved at defined sites to release the mature ribosomal RNAs, but the functions of many ribosome biogenesis factors involved in 18S rRNA release are not known. We apply an in vivo cross-linking technique coupled with deep sequencing (CRAC) that captures transcriptome-wide interactions between the yeast PIN domain protein Utp23 and its targets in a living cell. Methods: We apply CRAC to an HTP-tagged Utp23 protein (HTP: His6 - TEV cleavage site - two copies of the z-domain of Protein A) in budding yeast. At least two independent experiments were performed and analysed separately. A non-tagged yeast strain was also used as a negative control. Results: We found that yeast Utp23 UV-crosslinked in vivo to the snR30 snoRNA and to the eukaryotic-specific expansion segment 6 (ES6) in the 18S rRNA. Conclusion: According to our crosslinking data, Utp23 is perfectly positioned to coordinate release of the snR30 snoRNA from the 18S ES6 region.
2017-01-11 | GSE87238 | GEO
Project description:The eukaryotic ribosome is a complex molecular machine responsible for the translation of mRNA to protein. Faulty ribosome production leads to decreased protein production, increased cellular stress, and often cell death. How defective ribosomes are detected and cleared is poorly understood. We modeled ribosome biogenesis failure in human cells and performed CRISPRi screens to identify quality control factors that cope with trapped biogenesis intermediates. We identified ZNF574 as the top hit. ZNF574 contains Cys2-His2 (C2H2) zinc finger binding domains that are known to interact with both DNA and RNA, providing a potential mechanism for recognizing and engaging defective ribosomes. ZNF574 localizes in the nucleoplasm and cellular speckles, similar to late ribosome biogenesis factors like eIF6 and NMD3. We confirmed that depletion of ZNF574 impedes the degradation of faulty ribosomes. We performed immunoprecipitation followed by mass spectrometric analysis. Our immunoprecipitation of GFP-tagged ZNF574 followed by mass spectrometry analysis of interacting proteins revealed strong enrichment for ribosomal proteins from the large subunit. Together, our data show that ZNF574 functions as a quality control factor that targets defective large subunits.
2025-04-28 | PXD051645 | Pride
Project description:Bud22 binds to the 5´domain of 18S rRNA and U14 snoRNA Grant Number: BA 2316/2-1 German Research Foundation (DFG) Grantee: Jochen,,Baßler
2023-04-30 | GSE214203 | GEO
Project description:Eukaryotic ribosome biogenesis begins with the co-transcriptional assembly of the 90S pre-ribosome. The ‘U three protein’ (UTP) complexes and snoRNA particles arrange around the nascent pre-ribosomal RNA chaperoning its folding and further maturation. The earliest event in this hierarchical process is the binding of the UTP-A complex to the 5’-end of the pre-ribosomal RNA (5’-ETS). This oligomeric complex predominantly consists of β-propeller and α-solenoidal proteins. Here we present the structure of the Utp4 subunit from the thermophilic fungus Chaetomium thermophilum at 2.15 Å resolution and analyze its function by UV RNA-crosslinking (CRAC) and in context of a recent cryo-EM structure of the 90S pre-ribosome. Utp4 consists of two orthogonal and highly basic β-propellers that perfectly fit the EM-data. The Utp4 structure highlights an unusual Velcro-closure of its C-terminal β-propeller as relevant for protein integrity and Utp8 recognition in the context of the pre-ribosome. We provide a first model of the 5’-ETS RNA from an internally hidden 5’-end up to the region that hybridizes to the 3’-hinge sequence of U3 snoRNA and validate a specific Utp4/5’-ETS interaction by CRAC analysis. Altogether Utp4 is central to the UTP-A complex and organizes the 5’-ETS for further maturation.
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Project description:ZNF574 is a Quality Control Factor for Defective Ribosome Biogenesis Intermediates [CRISPRi_FLOW]
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Project description:ZNF574 is a Quality Control Factor for Defective Ribosome Biogenesis Intermediates [CRISPRi_growth]
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Project description:Post-transcriptional regulation of Ribosome Biogenesis
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Project description:Eukaryotic ribosome assembly is an intricate process that involves four ribosomal RNAs, 80 ribosomal proteins, and over 200 biogenesis factors that take part in numerous interdependent steps. The complexity and essentiality of this process creates opportunities for deleterious mutations to occur, accumulate, and impact downstream cellular processes. “Dead-end” ribosome intermediates that result from biogenesis errors are rapidly degraded, affirming the existence of quality control pathway(s) that monitor ribosome assembly. However, the factors that differentiate between on-path and dead-end intermediates are unknown. We engineered a system to perturb ribosome assembly in human cells and discovered that faulty ribosomes are degraded via the ubiquitin proteasome system. We identified ZNF574 as a key component of a novel quality control pathway, which we term the Ribosome Assembly Surveillance Pathway (RASP). In an animal model, loss of ZNF574 leads to developmental defects, further emphasizing the importance of RASP in organismal health.
2025-05-30 | GSE275991 | GEO
Project description:Eukaryotic ribosome assembly is an intricate process that involves four ribosomal RNAs, 80 ribosomal proteins, and over 200 biogenesis factors that take part in numerous interdependent steps. The complexity and essentiality of this process creates opportunities for deleterious mutations to occur, accumulate, and impact downstream cellular processes. “Dead-end” ribosome intermediates that result from biogenesis errors are rapidly degraded, affirming the existence of quality control pathway(s) that monitor ribosome assembly. However, the factors that differentiate between on-path and dead-end intermediates are unknown. We engineered a system to perturb ribosome assembly in human cells and discovered that faulty ribosomes are degraded via the ubiquitin proteasome system. We identified ZNF574 as a key component of a novel quality control pathway, which we term the Ribosome Assembly Surveillance Pathway (RASP). In an animal model, loss of ZNF574 leads to developmental defects, further emphasizing the importance of RASP in organismal health.
2025-05-30 | GSE275990 | GEO
Project description:The budding yeast E3 SUMO ligase Mms21, a component of the Smc5-6 complex, regulates sister chromatid cohesion, DNA replication, and DNA repair. We identify a role for Mms21 in ribosome biogenesis. The mms21RINGD mutant exhibits reduced rRNA production, nuclear accumulation of 60S and 40S ribosomal proteins, and elevated Gcn4 translation. Genes involved in ribosome biogenesis and translation are down-regulated in the mms21RINGD mutant. Examining gene expression profile of mms21RINGD mutant compared to wild-type by RNA Seq using Ilumina sequencing
2015-06-13 | E-GEOD-69826 | biostudies-arrayexpress