Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RECQ5 mediates pre-rRNA processing in nucleolus

ABSTRACT: explore the biological function of RECQ5 in nucleolus

ORGANISM(S): Homo Sapiens

SUBMITTER: Xiaochun Yu

PROVIDER: PXD058022 | iProX | Tue Nov 19 00:00:00 GMT 2024

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Publications

RECQ5 mediates pre-rRNA processing in nucleolus.

Ma Yidi Y Yu Xiaochun X

Nucleic acids research 20250801 15

RECQ5 is a member of the RECQ helicase family that maintains genomic stability. However, the molecular mechanism of RECQ5 in this biological process remains elusive. Here, we show that RECQ5 localizes in the dense fibrillar component of nucleolus and associates with several pre-rRNA processing factors. It recognizes pre-rRNA and is able to unwind double-stranded RNA in vitro. Loss of RECQ5 induces the accumulation of 47S, 30SL5', and 30S pre-rRNA, and the reduction of 21S pre-rRNA, suggesting th ...[more]

PMID: 40823811

Similar Datasets

The putative NTPase Fap7 mediates cytoplasmic 20S pre-rRNA processing through a direct interaction with Rps14.

Project description:One of the proteins identified as being involved in ribosome biogenesis by high-throughput studies, a putative P-loop-type kinase termed Fap7 (YDL166c), was shown to be required for the conversion of 20S pre-rRNA to 18S rRNA. However, the mechanism underlying this function has remained unclear. Here we demonstrate that Fap7 is strictly required for cleavage of the 20S pre-rRNA at site D in the cytoplasm. Genetic depletion of Fap7 causes accumulation of only the 20S pre-rRNA, which could be detected not only in 43S preribosomes but also in 80S-sized complexes. Fap7 is not a structural component of 43S preribosomes but likely transiently interacts with them by directly binding to Rps14, a ribosomal protein that is found near the 3' end of the 18S rRNA. Consistent with an NTPase activity, conserved residues predicted to be required for nucleoside triphosphate (NTP) hydrolysis are essential for Fap7 function in vivo. We propose that Fap7 mediates cleavage of the 20S pre-rRNA at site D by directly interacting with Rps14 and speculate that it is an enzyme that functions as an NTP-dependent molecular switch in 18S rRNA maturation.

| S-EPMC1291222 | biostudies-literature

A sliding-bulge structure at the Dicer processing site of pre-miRNA regulates alternative Dicer processing to generate 5’-isomiRs (pre-miR-203)

Project description:5’-isomiRs expand the repertoire of miRNA targets. However, how they are generated is not well understood. Here, we showed that, for some miRNAs in mammalian cells, 5’-isomiRs are generated by alternative Dicer processing by using miRNA offset RNAs (moRs) to determine Drosha cleavage sites in cells. In addition, we showed that in miR-203, alternative Dicer processing is regulated by a conserved sliding-bulge structure at the Dicer processing site, which allows the pre-miRNA molecule to fold into two different structures that are processed differently by Dicer. So far no RNA motif that slides to change conformation and alter a protein–RNA interaction has been reported. Thus, our study revealed a novel RNA motif that regulates 5’-isomiR generation in some miRNAs. It might also contribute to regulating protein–RNA interactions in other biological processes, since it takes only one point mutation to generate the sliding bulge, and there are a large number of different RNAs in the cell.

2016-09-01 | GSE80771 | GEO

Effect of depletion of Sas10 in pre-rRNA processing

Project description:Ribosome small subunit (SSU) is assembled by the SSU processome which contains approximately 70 non-ribosomal protein factors. The biochemical mechanism for the SSU processome in 18S rRNA processing and maturation has been extensively studied, however, how the SSU processome components enter to the nucleolus has not been systematically investigated. Here we checked the nucleolar localization of 50 human SSU processome components and find that UTP3 and other 24 proteins enter to the nucleolus autonomously. For the remaining 25 proteins we find that UTP3/SAS10 assists the nucleolar localization of five proteins, namely MPP10, UTP25, EMG1 and two UTP-B components UTP12 and UTP13, and this ferry function of UTP3 is conserved in zebrafish. We also find that knockdown of human UTP3 impairs the cleavage at A0-site while loss-of-function of either utp3/sas10 or utp13/tbl3 in zebrafish causes an accumulation of the processed products containing the 5′ETS, supporting the crucial role of UTP3 in mediating the 5′ETS processing and degradation. Moreover, UTP3 directly interacts with and delivers EXOSC10 into the nucleolus, suggesting that UTP3 may play a direct role in recruiting the nuclear exosome to the SSU processome for degradation of the processed 5′ETS. These findings lay the ground for studying the mechanism of cytoplasm-to-nucleolus trafficking of the SSU processome components and the multifaceted roles of UTP3 during pre-rRNA processing.

2024-09-18 | GSE262698 | GEO

SPTLC2 mediates AKT pathway and regulates the biological function of Ovarian Cancer

Project description:SPTLC2 mediates AKT pathway and regulates the biological function of Ovarian Cancer

| PRJNA1089504 | ENA

SPTLC2 mediates EGFR/STAT3 pathway regulates the biological function of Ovarian Cancer

Project description:SPTLC2 mediates EGFR/STAT3 pathway regulates the biological function of Ovarian Cancer

| PRJNA1090419 | ENA

Arabidopsis thaliana

Project description:Biological function of Pip3

| PRJNA120951 | ENA

NanoStringNormCNV: pre-processing of NanoString CNV data.

Project description:Summary:The NanoString System is a well-established technology for measuring RNA and DNA abundance. Although it can estimate copy number variation, relatively few tools support analysis of these data. To address this gap, we created NanoStringNormCNV, an R package for pre-processing and copy number variant calling from NanoString data. This package implements algorithms for pre-processing, quality-control, normalization and copy number variation detection. A series of reporting and data visualization methods support exploratory analyses. To demonstrate its utility, we apply it to a new dataset of 96 genes profiled on 41 prostate tumour and 24 matched normal samples. Availability and implementation:NanoStringNormCNV is implemented in R and is freely available at http://labs.oicr.on.ca/boutros-lab/software/nanostringnormcnv. Contact:paul.boutros@oicr.on.ca. Supplementary information:Supplementary data are available at Bioinformatics online.

| S-EPMC5860631 | biostudies-literature

Pantoea agglomerans strain:TB4

Project description:Biological Function Project (2004-2008)

| PRJDB18228 | ENA

Symbolic Processing Mediates the Relation Between Non-symbolic Processing and Later Arithmetic Performance.

Project description:The nature of the relation between non-symbolic and symbolic magnitude processing in the prediction of arithmetic remains a hotly debated subject. This longitudinal study examined whether the influence of non-symbolic magnitude processing on arithmetic is mediated by symbolic processing skills. A sample of 130 children with age-adequate (N = 73) or below-average (N = 57) achievement in early arithmetic was followed from the end of Grade 1 (mean age: 86.9 months) through the beginning of Grade 4. Symbolic comparison of one- and two-digit numbers serially mediated the effect of non-symbolic comparison on later arithmetic. These results support a developmental model in which non-symbolic processing provides a scaffold for single-digit processing, which in turn influences multi-digit processing and arithmetic. In conclusion, both non-symbolic and symbolic processing play an important role in the development of arithmetic during primary school and might be valuable long-term indicators for the early identification of children at risk for low achievement in arithmetic.

| S-EPMC7113405 | biostudies-literature

Human pre-60S assembly factors link rRNA transcription to pre-rRNA processing.

Project description:In eukaryotes, the nucleolus is the site of ribosome biosynthesis, an essential process in all cells. While human ribosome assembly is largely evolutionarily conserved, many of the regulatory details underlying its control and function have not yet been well-defined. The nucleolar protein RSL24D1 was originally identified as a factor important for 60S ribosomal subunit biogenesis. In addition, the PeBoW (BOP1-PES1-WDR12) complex has been well-defined as required for pre-28S rRNA processing and cell proliferation. In this study, we show that RSL24D1 depletion impairs both pre-ribosomal RNA (pre-rRNA) transcription and mature 28S rRNA production, leading to decreased protein synthesis and p53 stabilization in human cells. Surprisingly, each of the PeBoW complex members is also required for pre-rRNA transcription. We demonstrate that RSL24D1 and WDR12 co-immunoprecipitate with the RNA polymerase I subunit, RPA194, and regulate its steady state levels. These results uncover the dual role of RSL24D1 and the PeBoW complex in multiple steps of ribosome biogenesis, and provide evidence implicating large ribosomal subunit biogenesis factors in pre-rRNA transcription control.

| S-EPMC9808572 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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