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Updated: Feb 23, 2026
DNAzyme-dependent Analysis of rRNA 2’-O-Methylation
Published on: September 16, 2019
Identification of sites of 2'-O-methylation vulnerability in human ribosomal RNAs by systematic mapping
Sunny Sharma1, Virginie Marchand2, Yuri Motorin3,4
1RNA Molecular Biology and Center for Microscopy and Molecular Imaging (CMMI), Fonds National de la Recherche (F.R.S./FNRS) and Université Libre de Bruxelles (ULB), BioPark campus Gosselies, Belgium.
Abstract:
Ribosomal RNA modifications are important in optimizing ribosome function. Sugar 2'-O-methylation performed by fibrillarin-associated box C/D antisense guide snoRNAs impacts all steps of translation, playing a role in disease etiology (cancer). As it renders adjacent phosphodiester bonds resistant to alkaline treatment, 2'-O-methylation can be monitored qualitatively and quantitatively by applying next-generation sequencing to fragments of randomly cleaved RNA. We remapped all sites of 2'-O-methylation in human rRNAs in two isogenic diploid cell lines, one producing and one not producing the antitumor protein p53. We identified sites naturally modified only partially (confirming the existence in cells of compositionally distinct ribosomes with potentially specialized functions) and sites whose 2'-O-methylation is sensitive to p53. We mapped sites particularly vulnerable to a reduced level of the methyltransferase fibrillarin. The remarkable fact that these are largely sites of natural hypomodification provides initial insights into the mechanism of partial RNA modification. Sites where methylation appeared vulnerable lie peripherally on the 3-D structure of the ribosomal subunits, whereas the numerous modifications present at the core of the subunits, where the functional centers lie, appeared robustly made. We suggest that vulnerable sites of 2'-O-methylation are highly likely to undergo specific regulation during normal and pathological processes.
Insights
This study reveals how p53 influences ribosomal RNA (ribonucleic acid) 2'-O-methylation, a key modification for ribosome function and cancer. Certain methylation sites are sensitive to p53 levels and fibrillarin, offering insights into ribosome regulation.
Area of Science:
- Molecular Biology
- Genetics
- Biochemistry
Background:
- Ribosomal RNA (rRNA) modifications, particularly sugar 2 -O-methylation, are crucial for optimal ribosome function and impact translation.
- These modifications are guided by fibrillarin-associated box C/D small nucleolar RNAs (snoRNAs) and are implicated in disease, including cancer.
Purpose of the Study:
- To remap 2 -O-methylation sites in human rRNAs in cell lines with and without the antitumor protein p53.
- To investigate the influence of p53 on rRNA methylation patterns.
- To identify rRNA sites vulnerable to reduced levels of the methyltransferase fibrillarin.
Main Methods:
- Utilized next-generation sequencing on randomly cleaved RNA fragments to monitor 2 -O-methylation sites.
- Analyzed rRNA methylation in two isogenic diploid cell lines differing in p53 production.
- Mapped methylation sites sensitive to p53 levels and fibrillarin reduction.
Main Results:
- Identified partially modified rRNA sites, suggesting compositional ribosome heterogeneity and specialized functions.
- Discovered rRNA sites where 2 -O-methylation is sensitive to p53 levels.
- Mapped rRNA sites vulnerable to reduced fibrillarin, correlating with natural hypomodification.
- Observed that vulnerable methylation sites are located peripherally on ribosomal subunits, unlike robustly modified core sites.
Conclusions:
- p53 plays a regulatory role in specific rRNA 2 -O-methylation sites.
- Naturally hypomodified sites are likely targets for regulation during normal and pathological processes.
- The peripheral location of vulnerable sites suggests a mechanism for differential ribosome regulation.
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