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Nanopore Sequencing Reveals rRNA Modification Changes in Human Cells Experiencing Oxidative or Inflammatory Stress
Aaron M Fleming1, Cynthia J Burrows1
1Department of Chemistry, University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112-0850, United States.
ACS Chemical Biology
|May 27, 2026
Summary
Cellular stress alters ribosomal RNA (rRNA) modifications, impacting protein synthesis. This study reveals distinct rRNA modification patterns during oxidative and inflammatory stress, identifying universal stress markers and potential biomarkers for cellular health.
Area of Science:
- Molecular Biology
- Cellular Biology
- Genomics
Background:
- Ribosomal RNA (rRNA) modifications regulate protein synthesis but their dynamics under stress are unclear.
- Understanding epitranscriptomic changes during cellular stress is crucial for cell health and disease research.
Purpose of the Study:
- To map human rRNA epitranscriptomic marks under oxidative, inflammatory, and ferroptosis stress.
- To investigate the temporal dynamics and functional implications of rRNA modification changes during stress.
Main Methods:
- Nanopore direct RNA sequencing with modification-aware models (Dorado v5.2.0).
- Analysis of rRNA modifications in human cell lines subjected to various stress conditions.
- Mapping modification sites onto ribosome structure.
Main Results:
- Oxidative stress decreased modification occupancy, notably 18S Ψ573 and 18S m6A1832.
- Inflammatory stress induced acute hypermodifications and chronic hypomodifications at specific rRNA sites.
- Pseudouridine modifications 28S Ψ4296 and 28S Ψ4353 decreased across all stressors, identified as universal stress markers.
- Stress-induced rRNA modification changes were mapped to functional ribosome regions, including the decoding center and mitochondrial peptidyl transferase center.
Conclusions:
- Oxidative and inflammatory stress induce distinct, time-resolved remodeling of the human rRNA epitranscriptome.
- RRNA modifications can serve as biomarkers for cellular health during oxidative or inflammatory stress exposure.
- Stress-induced changes in rRNA modifications suggest mechanisms for ribosome reprogramming and attenuation of mitochondrial translation.
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