- S. Grosswendt
- N. Rajewsky
MicroRNAs appear to be involved in nearly all biological processes, as the large majority of protein coding genes are assumed to be regulated by one or several miRNAs. To exert their repressive function on translation and transcript stability, miRNAs guide Argonaute (AGO) proteins to partially complementary sites in target RNAs. A short hexamer of the miRNAs, called the seed, is especially involved in target binding and complementarity to the seed can be used to predict targets of miRNAs, albeit with considerable number of false predictions. Several biochemical methods have been developed to identify miRNA targets, amongst others crosslinking and immunoprecipitation approaches. These identify target sites at nucleotide resolution and can also directly tell which miRNA is binding, when the data is analyzed for miRNA:target site ligation products. This chapter will give an overview on the mechanism by which miRNAs exert their repressive function and on the experimental methods that have been used to identify their targets. We further discuss the potential of unambiguous identification of miRNA interactions by ligations in the brain, where an extraordinary high number of miRNAs are expressed and huma- or primate-specific miRNAs are of special interest.