microRNA target identification by RNA pull down with biotinylated microRNA mimics

New exciting experimental approaches to transcriptome-wide identification of microRNA binding sites are revealing surprising details about microRNA interaction with RNA targets. Approximately one out of five microRNA interactions occur without canonical perfect base pairing to the seed sequence. Instead they are often governed by imperfect binding to the center of the microRNA. One primate specific microRNA appears to follow completely different rules for target recognition that are not foreseen at all by current prediction tools. Read about how improved RNA pull down techniques with biotinylated microRNA mimics are transforming our understanding of microRNA biology. Introduction Central to the understanding of microRNA function is knowledge about the genes they regulate. Bioinformatic microRNA target predictions are complicated by the fact that microRNAs interact with their mRNA targets with only partial base complementarity and in addition that these interactions are influenced by local mRNA secondary structure. Most microRNA prediction tools work on the assumption that perfect Watson-Crick base pairing between residues 2-8 of the microRNA (also known as the seed) and a sequence in the 3’UTR of the target mRNA is required for RISC mediated silencing. These tools incorporate factors such as free energy release by binding and phylogenetic conservation of binding sites to improve confidence of predictions. Although such tools are very useful and accurately predict true microRNA targets, they are also known for generating predictions with a high false positive rate. Perhaps less appreciated, but potentially more important, is that such tools also have a significant false negative rate. It has been shown that microRNAs also regulate gene expression through non-canonical interactions with mRNA targets which are generally ignored by prediction tools (1). There are known examples of microRNAs regulating translation through base pairing of a central region of the microRNA with the mRNA target (2). Several recent papers provide a wealth of data showing that non-canonical microRNA interactions are frequent, diverse, functional and much more prevalent than previously appreciated (3-6). These important discoveries were achieved by ingenious experimental approaches to global detection of microRNA targets and these technologies are certain to have a great impact on our understanding of microRNA function. “ microRNA target predictions are associated with both high false positive and false negative rates Strategies for experimental microRNA target identification microRNA target identification often involves experiments in which changes to transcript abundancies in response to manipulation of microRNA activity is measured. This can be achieved by different types of genetic manipulation or by use of oligonucleotide based microRNA inhibitors and microRNA mimics. These are powerful and important methods, but the results are often confounded by side effects of transfection and secondary effects of the change in microRNA activity. microRNAs may directly or indirectly affect the activity of multiple transcription factors which in turn can have profound effects on transcription that are not the direct result of microRNA interaction with mRNA targets. In addition, microRNA regulation of gene expression is often quite subtle at the transcriptional level and is best appreciated by measuring the abundance of the corresponding gene products.