Micro RNA detection

Only recently discovered, microRNAs (miRNAs) are small RNA gene products that regulate the activity of messenger RNAs by antisense base pairing. They thus constitute an astonishing further layer of gene expression regulation. Most of the miRNA genes discovered so far are involved in the regulation of developmental processes; many target transcription factors. Micro RNAs have been discovered in many animals (C. elegans, mouse, human) and plants (arabidopsis, rice, poplar) but plant and animal miRNAs differ significantly..

Goal of our research project is the discovery of new miRNAs by comparative phylogenetic analysis in the arabidopsis, poplar and rice genomes aided by cDNA libraries. We cooperate closely with Detlef Weigel's group at the MPI of developmental biology where biological validation of predicted miRNA candidates can be performed.

Many miRNAs are crucial for normal development: The healthy plant (arabidopsis) on the left has developed normally whereas the plant on the right is a mutant lacking an important miRNA.

One distinct characteristic of a miRNA gene is that its transcript is able to fold into a stem-loop structure as shown above - the so-called miRNA precursor. The actual miRNA (highlighted in red) is cut out of this precursor by a key enzyme called DICER.

For detection, we exploit this property by folding whole chromosomes on the RNA level and calculating corresponding base pairing probability matrices (shown on the right). The diagonal in the lower right corner emerges from the stem-loop structure an the right side of the predicted fold (shown on left).

Further characteristics of miRNAs are exploited: e.g. a miRNA's targets are typically close phylogenetic relatives. The red genes shown here a targeted by one miRNA family.