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Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms
Published on: September 13, 2018
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RNA marker modifications reveal the necessity for rigorous preparation protocols to avoid artifacts in
Florian Richter1, Johanna E Plehn1, Larissa Bessler1
1Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5 55128 Mainz, Germany.
Nucleic Acids Research
|December 1, 2021
Summary
RNA degradation after cell death introduces artefacts, impacting epitranscriptome analysis. Careful tissue preparation is crucial to avoid misinterpreting RNA modifications, especially in small RNAs and tRNAs.
Area of Science:
- Molecular Biology
- Epigenetics
- RNA Biology
Background:
- Accurate epitranscriptome definition is challenged by RNA degradation artefacts post-mortem.
- RNA degradation is a ubiquitous, understudied process impacting RNA modification analysis.
Purpose of the Study:
- To investigate artefacts in RNA modification analysis caused by post-mortem RNA degradation.
- To identify the impact of tissue preparation protocols on RNA modification patterns.
Main Methods:
- Tracing RNA marker modifications (m6,6A, Am) through tissue preparation.
- Analyzing mouse tissues at various post-mortem time points.
- Correlating RNA integrity with rRNA marker levels and tRNA modifications.
Main Results:
- RRNA degradation products, including m6,6A and Am, contaminate small RNA fractions.
- Significant differences in RNA degradation and modification patterns were observed between liver and brain tissues.
- RNA integrity correlated inversely with rRNA marker content and positively with informative tRNA modifications.
Conclusions:
- Post-mortem RNA degradation introduces significant artefacts into epitranscriptome analysis, particularly affecting small RNAs and tRNAs.
- Meticulous tissue and RNA preparation are essential to avoid misinterpreting RNA modification patterns.
- Validated RNA preparations allow for distinguishing even closely related brain tissues based on tRNA modifications.
