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Bias in recent miRBase annotations potentially associated with RNA quality issues

Nicole Ludwig1, Meike Becker2, Timo Schumann3

  • 1Department of Human Genetics, Saarland University, Homburg, Germany. n.ludwig@mx.uni-saarland.de.

Scientific Reports
|July 14, 2017
PubMed

Insights

RNA degradation significantly distorts microRNA expression patterns in mouse liver tissue. Many microRNAs, especially recent miRBase entries, may be artefacts, impacting biomarker research.

Area of Science:

  • Molecular Biology
  • Genomics
  • Biomarker Research

Background:

  • MicroRNAs (miRNAs) are crucial small non-coding RNAs involved in gene regulation.
  • In vivo stability of miRNAs is assumed, but degradation processes can affect their detection.
  • Distorted miRNA patterns can arise from various experimental factors, including sample handling.

Purpose of the Study:

  • To quantify the impact of RNA degradation on miRNA expression in mouse liver.
  • To identify specific causes of distorted miRNA profiles.
  • To differentiate between true and artefactual miRNA signals.

Main Methods:

  • Analysis of miRNA expression in mouse liver samples with varying RNA integrity.
  • Correlation analysis between miRNA levels and storage conditions (room temperature, 4°C).
  • Next-generation sequencing (NGS) to detect potential cross-hybridization signals.

Main Results:

  • Significant correlations found between miRNA expression and RNA integrity (298 miRNAs), room temperature storage (99 miRNAs), and 4°C storage (8 miRNAs).
  • 226 miRNAs showed >2-fold expression differences between high and low RNA integrity samples.
  • 350 miRNAs detected in degraded RNA suggested cross-hybridization, with 157 recent miRBase entries showing increased expression in low-integrity samples.

Conclusions:

  • RNA degradation is a significant confounder in miRNA expression studies.
  • Recently annotated miRNAs in miRBase are particularly susceptible to artefactual detection due to degradation.
  • Distinguishing degradation-sensitive and artefactual miRNAs is crucial for reliable miRNA biomarker discovery and application.

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