ArticleNucleic acids research2022
RNA marker modifications reveal the necessity for rigorous preparation protocols to avoid artifacts in epitranscriptomic analysis.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Harmonized nucleoside mass spectrometry enables reproducible cross-platform RNA modification quantification.bioRxiv : the preprint server for biology · 2026Article
- tRNA modification profiling reveals epitranscriptome regulatory networks in Pseudomonas aeruginosa.Nucleic acids research · 2025Article
- Global analysis by LC-MS/MS ofRNA (New York, N.Y.) · 2025Article
- The role of m5C, m1A and m7G modifications in tumors of urinary system.Frontiers in cell and developmental biology · 2025Review
- DORQ-seq: high-throughput quantification of femtomol tRNA pools by combination of cDNA hybridization and Deep sequencing.Nucleic acids research · 2024Article
- Analysis of RNA and Its Modifications.Annual review of analytical chemistry (Palo Alto, Calif.) · 2024Review
- Altered landscape of total RNA, tRNA and sncRNA modifications in the liver and spleen of mice infected by Toxoplasma gondii.PLoS neglected tropical diseases · 2024Article
- Mass Spectrometry-Based Pipeline for Identifying RNA Modifications Involved in a Functional Process: Application to Cancer Cell Adaptation.Analytical chemistry · 2024Article
- ExploringHorticulture research · 2024Article
- Ribonucleosides from tRNA in hyperglycemic mammalian cells and diabetic murine cardiac models.Life sciences · 2023Article
- ALL-tRNAseq enables robust tRNA profiling in tissue samples.Genes & development · 2023Article
- Quantification of substoichiometric modification reveals global tsRNA hypomodification, preferences for angiogenin-mediated tRNA cleavage, and idiosyncratic epitranscriptomes of human neuronal cell-lines.Computational and structural biotechnology journal · 2023Article
- Experimental and computational workflow for the analysis of tRNA pools from eukaryotic cells by mim-tRNAseq.STAR protocols · 2022Article
- Opportunities and Challenges to Profile mRNA Modifications in Escherichia coli.Chembiochem : a European journal of chemical biology · 2022Article
- Multivariate Analysis of RNA Chemistry Marks Uncovers Epitranscriptomics-Based Biomarker Signature for Adult Diffuse Glioma Diagnostics.Analytical chemistry · 2022Article
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9 authors.
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Abstract
The accurate definition of an epitranscriptome is endangered by artefacts resulting from RNA degradation after cell death, a ubiquitous yet little investigated process. By tracing RNA marker modifications through tissue preparation protocols, we identified a major blind spot from daily lab routine, that has massive impact on modification analysis in small RNAs. In particular, m6,6A and Am as co-varying rRNA marker modifications, appeared in small RNA fractions following rRNA degradation in vitro and in cellulo. Analysing mouse tissue at different time points post mortem, we tracked the progress of intracellular RNA degradation after cell death, and found it reflected in RNA modification patterns. Differences were dramatic between liver, where RNA degradation commenced immediately after death, and brain, yielding essentially undamaged RNA. RNA integrity correlated with low amounts of co-varying rRNA markers. Thus validated RNA preparations featured differentially modified tRNA populations whose information content allowed a distinction even among the related brain tissues cortex, cerebellum and hippocampus. Inversely, advanced cell death correlated with high rRNA marker content, and correspondingly little with the naïve state of living tissue. Therefore, unless RNA and tissue preparations are executed with utmost care, interpretation of modification patterns in tRNA and small RNA are prone to artefacts.
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