MicroRNAs (miRNAs) are endogenous 22-nt long non-coding RNAs that regulate gene expression post-transcriptionally in a diversity of organisms (Bartel, 2004). Although the understanding of miRNA biological functions is progressing remarkably, the exact mechanisms by which miRNAs regulate gene expression are still not unambiguously defined. However, it is commonly believed that miRNAs trigger target mRNA regulation by binding to 3’UTRs (Chekulaeva & Filipowicz, 2009). The discovery of the first miRNA (lin-4) revealed sequence complementarity to multiple conserved sites in the 3’UTR of the lin-14 mRNA (Lee et al., 1993; Wightman et al., 1993). Exact principles of gene expression knockdown mediated by miRNA are still in debate (Eulalio et al., 2008). Binding site properties have an essential impact on miRNA-mRNA interaction. Rational design of binding sites could thereby help to achieve a narrow range of knockdown. The applicability is still limited by redundant target sites and various miRNA expression patterns within the cells which are hardly to measure. The experimental identification and/or validation of miRNA targets by means of proteomic or transcriptomic studies, reporter gene assays or over-expression/knockdown analysis is necessary to understand the biological relevance of the miRNA-mRNA interaction. Although progressively improving, even the reliability of in silico target prediction tools is still far away from being precise.
With our Synthetic miRNA Kit we can make not only make use of the miRNA properties mentioned above; additionally, a big part of our project aims at the characterization of binding site sequences. Some functionally important parts of miRNAs have been described in literature, such as the seed region. The seed region is defined as a region of seven nucleotides that show perfect pairing between the miRNA and its target sequence. The seed usually consists of the nucleotides 2-8 of a miRNA binding sites (Grimson et al., 2007; Bartel, 2009). Based on this simple principle, we randomized our miRNA binding sites between nucleotide 9 and 12 or 9 and 22 or tried rational exchanges of nucleotides to see how they would effect binding of the miRNA, e. g. replacing one purin base with another versus replacing it with a pyrimidin base. A more detail description of the different binding sites we characterized can be found in our measurements page. After creating a binding site library and testing the miRNA-binding site interaction in vitro, we were able to compute an in silico model based on a machine learning approach.
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