RNA degradation compromises the reliability of microRNA expression profiling.
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.


CONCLUSIONS
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.
Ibberson
David
D
Genomics Core Facility, EMBL, Meyerhofstrasse 1 D-69117 Heidelberg, Germany. ibberson@embl.de
Benes
Vladimir
V
Muckenthaler
Martina U
MU
Castoldi
Mirco
M
D000818:Animals; D016000:Cluster Analysis; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D051379:Mice; D035683:MicroRNAs / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D020871:RNA Stability; D020133:Reverse Transcriptase Polymerase Chain Reaction
D035683:MicroRNAs