Bias in recent miRBase annotations potentially associated with RNA quality issues.

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.