MicroRNA Labeling Methods Directly Influence the Accuracy of Expression Profiling Detection

MicroRNA (miRNA) expression profiling is a powerful and commonly used methodology for assessing the relative levels of individual miRNAs in specific tissues. To achieve accurate results using miRNA microarray detection strategies, it is important that all sample miRNA species are representatively labeled prior to the hybridization step. In this study, we compared the expression profiles of miRNAs labeled using enzymatic methods and a direct chemical labeling method. Using miRNA samples isolated from mouse brain and heart in a comparative microarray analysis, we show that some specific miRNAs are not detected when enzymatic tailing methods are used; however they are detected with the Label IT® chemical labeling method. The presence of the discrepant miRNAs in the model mouse tissues was corroborated by northern blot analysis and confirmed by qRT-PCR. Thus, miRNA expression profiles generated by enzymatic labeling methods (poly(A) polymerase tailing) may not be representative for all miRNAs that are present...