PXD047506

PXD047506 is an original dataset announced via ProteomeXchange.

Title	The novel pre-rRNA detection workflow “Riboprobing” identified a hitherto undescribed aberrant pre-rRNA
Description	Ribosomes translate mRNA into proteins and are essential for every living organism. In eukaryotes both ribosomal subunits are rapidly assembled in a strict hierarchical order, starting in the nucleolus with transcription of a common precursor ribosomal RNA (pre-rRNA). This pre-rRNA encodes three of the four mature rRNAs which are formed by several, consecutive endonucleolytic and exonucleolytic processing steps. Historically, Northern Blots are used to analyze the variety of different pre-rRNA species, only allowing rough length estimations. Although this limitation can be overcome with Primer Extension, both approaches often use radioactivity and are time consuming and costly. Here we present “Riboprobing” a reverse transcription-based workflow extended by linker ligation for easy and fast detection and characterization of various pre-rRNA species and their 5` as well as 3` ends. Using standard molecular biology lab equipment, our technique allows reliable discrimination of pre-rRNA species not resolved by Northern Blotting (e.g.: 27SA2, 27SA3 and 27SB). The method can be successfully used for analysis of total cell extracts as well as purified pre-ribosomes for a straightforward evaluation of the impact of mutant gene versions or inhibitors. In the course of method development, we identified and characterized a hitherto undescribed aberrant pre-rRNA, arising from LiCl inhibition. This pre-rRNA fragment spans from processing site A1 to E, forming a small RNP that is lacking most early joining assembly factors. This finding expands our knowledge of how the cell deals with severe pre-rRNA processing defects and demonstrates the strict requirement for the 5’ETS for the assembly process.
HostingRepository	PRIDE
AnnounceDate	2025-04-29
AnnouncementXML	Submission_2025-04-29_01:31:55.692.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Juliane Merl-Pham
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2023-12-04 06:21:08	ID requested
⏵ 1	2025-04-29 01:31:56	announced

10.1261/RNA.079912.123;

submitter keyword: aberrant pre-rRNA, Primer Extension,Ribosome biogenesis, Reverse Transcription, pre-rRNA processing

Helmut Bergler
contact affiliation	Institute of Molecular Biosciences, University of Graz, Graz, 8010, Austria; BioTechMed-Graz, Graz, Austria
contact email	helmut.bergler@uni-graz.at
lab head
Juliane Merl-Pham
contact affiliation	Metabolomics and Proteomics Core, Helmholtz Munich
contact email	juliane.merl@helmholtz-muenchen.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/04/PXD047506

PRIDE project URI

• PRIDE
  1. PXD047506
     1. Label: PRIDE project
     2. Name: The novel pre-rRNA detection workflow “Riboprobing” identified a hitherto undescribed aberrant pre-rRNA