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Open Access Highly Accessed Methodology article

RNA degradation compromises the reliability of microRNA expression profiling

David Ibberson1, Vladimir Benes1, Martina U Muckenthaler23 and Mirco Castoldi23*

Author Affiliations

1 Genomics Core Facility, EMBL, Meyerhofstraße 1 D-69117 Heidelberg, Germany

2 Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Im Neuenheimer Feld 156, D-69120, Heidelberg, Germany

3 Molecular Medicine Partnership Unit, Im Neuenheimer Feld 156, D-69120, Heidelberg, Germany

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BMC Biotechnology 2009, 9:102  doi:10.1186/1472-6750-9-102

Published: 21 December 2009

Abstract

Background

MicroRNAs are small non-coding RNAs that post-transcriptionally regulate gene expression and their expression is frequently altered in human diseases, including cancer. To correlate clinically relevant parameters with microRNA expression, total RNA is frequently prepared from samples that were archived for various time periods in frozen tissue banks but, unfortunately, RNA integrity is not always preserved in these frozen tissues. Here, we investigate whether experimentally induced RNA degradation affects microRNA expression profiles.

Results

Tissue samples were maintained on ice for defined time periods prior to total RNA extraction, which resulted in different degrees of RNA degradation. MicroRNA expression was then analyzed by microarray analysis (miCHIP) or microRNA-specific real-time quantitative PCR (miQPCR). Our results demonstrate that the loss of RNA integrity leads to in unpredictability of microRNA expression profiles for both, array-based and miQPCR assays.

Conclusion

MicroRNA expression cannot be reliably profiled in degraded total RNA. For the profiling of microRNAs we recommend use of RNA samples with a RNA integrity number equal to or above seven.