University of Copenhagen

The aim of the Wilhelm Johannsen Centre for Functional Genome Research is to contribute to the functional characterization of the human genome by identification of novel human disease genes, of novel genetic entities and of novel genetic mechanisms by systematic mapping and characterization of chromosomal and genomic rearrangements associated with abnormal and normal phenotypes.

High throughput sequencing facility at Wilhelm Johannsen Centre

Wilhelm Johannsen Centre has been generously funded by The Lundbeck Foundation to obtain the first second generation version of the Illumina Genome Analyzer GAII, with paired-end facility, in Denmark. With its capacity to sequence close to 100 million clones corresponding to more than 3 billion basepairs in one run, and with the prospects that this capacity will be more than trippled in the near future, the platform will become a major resource for our future research strategy. Apart from approaching the capacity needed for whole genome sequencing, the potential of the technology for digital expression analysis, resequencing of specific genomic regions and candidate disease genes, and genome wide analysis of DNA methylation, transcription factor binding sites (CHiP-Seq) and other applications where DNA/RNA can be isolated in a biological menaingful way, will be vast. The platform has been successfully installed. Potential collaborators who want to know more about the possibilites should contact Niels Tommerup.

Detection of microRNAs in frozen tissue sections

The ability to determine spatial and temporal microRNA (miRNA) accumulation at the tissue, cell and subcellular levels is essential for understanding the biological roles of miRNAs and miRNA-associated gene regulatory networks. In the latest number of Nature Protocols a research group led by Asli Silahtaroglu at the Wilhelm Johannsen Centre for Functional Genome Research describe a method for fast and effective detection of miRNAs in frozen tissue sections using fluorescence in situ hybridization (FISH). The method combines the unique miRNA recognition properties of locked nucleic acid (LNA)-modified oligonucleotide probes with FISH using the tyramide signal amplification (TSA) technology. Although both approaches have previously been shown to increase detection sensitivity in FISH, combining these techniques into one protocol significantly decreases the time needed for miRNA detection in cryosections, while simultaneously retaining high detection sensitivity. Starting with fixation of the tissue sections, this miRNA FISH protocol can be completed within approximately 6 h and allows miRNA detection in a wide variety of animal tissue cryosections as well as in human tumor biopsies at high cellular resolution.