Proteomic analysis of PELP1 (RIX1) interactome.
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Exploris 480
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
Catherine Denicourt
PROVIDER: MSV000096583 | MassIVE | Tue Dec 03 17:14:00 GMT 2024
REPOSITORIES: MassIVE
Similar Datasets
Project description:The Drosha-DGCR8 complex (Microprocessor) is required for microRNA (miRNA) biogenesis. DGCR8 contains two double-stranded RNA binding motifs that recognize the RNA substrate, whereas Drosha functions as the endonuclease. We have used high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) to identify endogenous RNA targets of DGCR8 in mammalian cells. Unexpectedly, miRNAs were not the most abundant targets. DGCR8-bound RNAs comprised several hundred mRNAs as well as snoRNAs and long non-coding RNAs. We found that DGCR8 together with Drosha controls the abundance of several mRNAs, as well as long non-coding RNAs, such as MALAT-1. By contrast, the DGCR8-mediated cleavage of snoRNAs is independent of Drosha, suggesting the involvement of DGCR8 in cellular complexes with other endonucleases. Interestingly, binding of DGCR8 to cassette exons, acts as a novel mechanism to regulate the relative abundance of alternatively spliced isoforms. Collectively, these data provide new insights in the complex role of DGCR8 in controlling the fate of several classes of RNAs. Comparison of RNAs associated to both endogenous (D8) and overexpressed (T7) DGCR8 in HEK293T cells
2012-07-15 | E-GEOD-39086 | biostudies-arrayexpress
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
Project description:Cancer cells frequently upregulate ribosome production to support tumorigenesis. While small nucleolar RNAs (snoRNAs) are critical for ribosome biogenesis, the roles of other classes of noncoding RNAs in this process remain largely unknown. Here we performed CRISPR screens to identify essential long noncoding RNAs (lncRNAs) in renal cell carcinoma (RCC) cells. This revealed that an alternatively-spliced isoform of lncRNA Colorectal Neoplasia Differentially Expressed containing an ultraconserved element (UCE), referred to as CRNDEUCE, is required for RCC cell proliferation. CRNDEUCE localizes to the nucleolus and promotes 60S ribosomal subunit biogenesis. The UCE of CRNDE functions as an unprocessed C/D box snoRNA that directly interacts with ribosomal RNA precursors. This facilitates delivery of eIF6, a key 60S biogenesis factor, which binds to CRNDEUCE through a sequence element adjacent to the UCE. These findings highlight the functional versatility of snoRNA sequences and expand the known mechanisms through which noncoding RNAs orchestrate ribosome biogenesis.
2025-03-24 | GSE270849 | GEO
Project description:Cancer cells frequently upregulate ribosome production to support tumorigenesis. While small nucleolar RNAs (snoRNAs) are critical for ribosome biogenesis, the roles of other classes of noncoding RNAs in this process remain largely unknown. Here we performed CRISPR screens to identify essential long noncoding RNAs (lncRNAs) in renal cell carcinoma (RCC) cells. This revealed that an alternatively-spliced isoform of lncRNA Colorectal Neoplasia Differentially Expressed containing an ultraconserved element (UCE), referred to as CRNDEUCE, is required for RCC cell proliferation. CRNDEUCE localizes to the nucleolus and promotes 60S ribosomal subunit biogenesis. The UCE of CRNDE functions as an unprocessed C/D box snoRNA that directly interacts with ribosomal RNA precursors. This facilitates delivery of eIF6, a key 60S biogenesis factor, which binds to CRNDEUCE through a sequence element adjacent to the UCE. These findings highlight the functional versatility of snoRNA sequences and expand the known mechanisms through which noncoding RNAs orchestrate ribosome biogenesis.
2025-03-24 | GSE270848 | GEO
Project description:Cancer cells frequently upregulate ribosome production to support tumorigenesis. While small nucleolar RNAs (snoRNAs) are critical for ribosome biogenesis, the roles of other classes of noncoding RNAs in this process remain largely unknown. Here we performed CRISPR screens to identify essential long noncoding RNAs (lncRNAs) in renal cell carcinoma (RCC) cells. This revealed that an alternatively-spliced isoform of lncRNA Colorectal Neoplasia Differentially Expressed containing an ultraconserved element (UCE), referred to as CRNDEUCE, is required for RCC cell proliferation. CRNDEUCE localizes to the nucleolus and promotes 60S ribosomal subunit biogenesis. The UCE of CRNDE functions as an unprocessed C/D box snoRNA that directly interacts with ribosomal RNA precursors. This facilitates delivery of eIF6, a key 60S biogenesis factor, which binds to CRNDEUCE through a sequence element adjacent to the UCE. These findings highlight the functional versatility of snoRNA sequences and expand the known mechanisms through which noncoding RNAs orchestrate ribosome biogenesis.
2025-03-24 | GSE270847 | 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.
2015-06-13 | GSE69826 | GEO
Project description:Assembly of eukaryotic ribosomes begins in the nucleolus, a compartmentalized membraneless organelle. Although the two ribosomal subunits, 40S and 60S, assemble independently, it remains unknown if these particles are physically sorted as they assemble and how they partition from the central chromatin compartment into the outer nucleolar regions, where maturation occurs. In this study, we show that nucleophosmin specifically mediates the assembly of nascent 60S subunits and that this specificity is determined by its chromatin localization at the rDNA sites encoding for 60S subunit rRNA. Nucleophosmin dissociates from chromatin to bind nascent 60S subunits, causing their partitioning away from chromatin and from nascent 40S subunits through liquid-liquid phase separation. This directs translocation of nascent 60S subunits towards the nucleophosmin-rich granular component, where biogenesis continues. Notably, this compartmentalization increases the efficiency of 60S subunit assembly, specifically the incorporation of the 60S domain III. Our data reveal that the chromatin localization of nucleophosmin determines its specificity in sorting and coordinates the movement of ribosomal subunits into specialized assembly compartments.
2023-03-01 | GSE156203 | 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. Previous research on ribosome biogenesis primarily focused on factors facilitating the proper assembly of the ribosome. By contrast, investigations into quality control mechanisms targeting abnormal pre-ribosomes remain relatively unexplored. We established a method to impede the maturation of a small subset of ribosomes in human cells. The assembly of the 60S large ribosomal subunit begins in the nucleolus, continues through the nucleoplasm, and concludes in the cytoplasm with the incorporation of the ribosomal protein uL16/RPL10 and the release of the late-acting biogenesis factors. We designed a system where incorporation of a mutant uL16 lacking residues 102-111 blocks the assembly of the maturing large subunit. To confirm that uL16mut incorporation blocks 60S maturation, we purified tagged uL16wt or uL16mut and identified associated proteins via western blotting and mass spectrometry analysis. We did not detect an interaction between uL16mut-containing large and subunits small subunit proteins, validating that the 60Smut subunits are trapped during biogenesis and unable to pair with small subunits to engage in active translation. We observed significant enrichment of late ribosome biogenesis factors, such as eIF6 and NMD3, upon uL16mut immunoprecipitation.
2025-04-28 | PXD051646 | Pride
Project description:The alpha7 nicotinic acetylcholine receptor (nAChR) is well established as the principal high-affinity alpha-bungarotoxin-binding protein in the mammalian brain. We isolated carbachol-sensitive alpha-bungarotoxin-binding complexes from total mouse brain tissue by affinity immobilization followed by selective elution, and these proteins were fractionated by SDS-PAGE. The proteins in subdivided gel lane segments were tryptically digested, and the resulting peptides were analyzed by standard mass spectrometry. We identified 55 proteins in wild-type samples that were not present in comparable brain samples from alpha7 nAChR knockout mice that had been processed in a parallel fashion. Many of these 55 proteins are novel proteomic candidates for interaction partners of the alpha7 nAChR, and many are associated with multiple signaling pathways that may be implicated in alpha7 function in the central nervous system. The newly identified potential protein interactions, together with the general methodology that we introduce for alpha-bungarotoxin-binding protein complexes, form a new platform for many interesting follow-up studies aimed at elucidating the physiological role of neuronal alpha7 nAChRs.
| S-EPMC2891571 | biostudies-literature
Project description:Breast cancer is the most frequently diagnosed malignant neoplasm and the second leading cause of cancer death among women. Epithelial-to-mesenchymal Transition (EMT) plays a critical role in the organism development, providing cell migration and tissue formation. However, its erroneous activation in malignancies can serve as the basis for the dissemination of cancer cells and metastasis. The Zeb1 transcription factor, which regulates the EMT activation, has been shown to play an essential role in malignant transformation. This factor is involved in many signaling pathways that influence a wide range of cellular functions via interacting with many proteins that affect its transcriptional functions. Importantly, the interactome of Zeb1 depends on the cellular context. Here, using the inducible expression of Zeb1 in epithelial breast cancer cells, we identified a substantial list of novel potential Zeb1 interaction partners, including proteins involved in the formation of malignant neoplasms, such as ATP-dependent RNA helicase DDX17and a component of the NURD repressor complex, CTBP2. We confirmed the presence of the selected interactors by immunoblotting with specific antibodies. Further, we demonstrated that co-expression of Zeb1 and CTBP2 in breast cancer patients correlated with the poor survival prognosis, thus signifying the functionality of the Zeb1-CTBP2 interaction.
| S-EPMC8197395 | biostudies-literature