Genome sequencing has shown that the complexity of an organism is not primarily determined by the number of genes, but rather by the diversity of how these genes are regulated and processed. In particular non-protein-coding RNAs (ncRNA) have been shown to be involved in important aspects of gene regulation, including chromatin silencing, alternative splicing, RNA editing, mRNA cleavage and translational suppression. One class of ncRNAs, the microRNAs (miRNA), comprises hundreds of genes that may target th ousands of messages for sequence-specific gene regulation. These RNA genes are important for tissue-specific gene regulation, and may be involved in disease onset, e.g. as oncogenes. Many aspects are poorly understood. Most of the regulatory miRNA targets are still unknown, and we need better tools for target identification. The regulation of the miRNA genes themselves is also poorly understood, in particular how distant enhancers may affect gene regulation.We are initiating a close collaboration betwee n the Norwegian University of Science and Technology (NTNU, Trondheim), the Sars Center (Bergen) and the Computational Biology Unit (CBU) at the University of Bergen (UoB) to elucidate the regulatory mechanisms involving ncRNA molecules, in particular miR NA, using a combination of bioinformatic and experimental approaches. The collaboration involves the FUGE Bioinformatics platform at NTNU and UoB. The zebrafish will be used as model system. This will allow us to study all aspects of miRNA function, makin g novel data as well as verification of bioinformatic predictions. The bioinformatic approaches will include novel evolutionary methods developed at Interagon AS, as well as ongoing research at NTNU and UoB.The project is organised as five integrated su b-projects, realised as PhD-projects. The results from this project will be highly relevant to medical research, e.g. for understanding genetic diseases involving non-protein-coding regions of the human genome.