Potential pitfalls in microRNA profiling

Department of Microbiology, UNC-Chapel Hill, Chapel Hill, NC, USA.
WIREs RNA (Impact Factor: 6.02). 09/2012; 3(5):601-16. DOI: 10.1002/wrna.1120
Source: PubMed


MicroRNAs (miRNAs) are small, noncoding RNAs that post-transcriptionally influence a wide range of cellular processes such as the host response to viral infection, innate immunity, cell cycle progression, migration, and apoptosis through the inhibition of target mRNA translation. Owing to the growing number of miRNAs and identification of their functional roles, miRNA profiling of many different sample types has become more expansive, especially with relevance to disease signatures. In this review, we address some of the advantages and potential pitfalls of the currently available methods for miRNA expression profiling. Some of the topics discussed include isomiRNAs, comparison of different profiling platforms, normalization strategies, and issues with regard to sample preparation and experimental analyses. WIREs RNA 2011 DOI: 10.1002/wrna.1120
For further resources related to this article, please visit the WIREs website.

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Available from: Dirk P Dittmer, Apr 26, 2014
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    • "We found a significant up-regulation of miR-215-5p in the DOXY cell line compared to the control HepG2 tet-on cell line (0.2 fold, p = 0.04). We also normalised against the commonly used RG U6 and found miR-215-5p tothe use of this specific spliceosomal RNA as RG in microRNA studies because of its variability in structure and abundance as well as its often high degree of variance across samples[19,20,41,42]. Our study demonstrates the importance of correct normalisation in microRNA expression studies, where even small changes in expression can have a vast downstream effect[5]. "
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    • "For Taqman ® human microRNA cards, the small nuclear RNA (snRNA) U6 and the small nucleolar RNAs (snoRNAs) RNU44 and RNU48 are recommended as endogenous controls based on healthy tissue and tumor cell line studies (NCI-60). However, these small RNAs have different biological und biochemical characters[14]compared to microRNAs and extraction quality, reverse transcription and PCR amplification may differ also from that of microRNAs[14,15]. Since normalization to small RNAs could therefore introduce bias, endogenous controls belonging to the same class of RNAs are likely more suitable housekeepers. "
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