Research

Research at our department

Sequencing of the complete human genome revealed that only a very small proportion of the genetic information is protein coding. Approximately 90% of the human genome, however, is not protein coding and was initially considered to be some kind of evolutionary ‘junk-DNA’. Today, we know that almost all non-coding DNA is actively transcribed to RNA and that such RNA molecules are very important for many cellular processes. Intensive research during the last years revealed that non-coding RNAs are involved in the regulation of different diseases like neurodegenerative diseases or cancer. The investigation of these RNAs is just at its beginning and future studies will certainly result in new prospects for cancer research.

Our research is focused on the investigation of non-coding RNA pathways in mammalian cells. Small RNAs such as short interfering RNAs (siRNAs) or microRNAs (miRNAs) are processed from double stranded (ds) precursor molecules by the action of RNase III enzymes. MiRNAs utilize the enzymes Drosha and Dicer while siRNAs typically only need Dicer processing from long dsRNA species. Both classes are single stranded small RNAs that are incorporated into the RNA-induced silencing complex (RISC). The direct binding partner of the small RNA is a member of the Argonaute protein family, which has been subject of our research for the past ten years. In current projects, we investigate posttranslational modifications of key miRNA biogenesis as well as effector proteins. Which signaling pathways and which kinases or phosphatases act on these factors? What are the biological consequences of phosphorylation at specific sites? These are two key questions in this project (see 1).

In parallel to the biochemical characterization of small RNA pathways in mammalian cells, we use RNA cloning and deep sequencing to profile short and long non-coding RNAs in cancer. In close collaboration with the medical faculty (Christina Hackl), we investigate non-coding RNAs in colorectal cancer progression. Together with Peter Hau, we profile non-coding RNA in glioblastoma patients (see 2).

In addition, we have started to identify and characterize RNA binding proteins that interact with specific miRNA precursor molecules. Using biochemical approaches, we identified hundreds of such proteins that sequence-specifically bind to pre-miRNAs. We are currently investigating the biological functions of these proteins. We employ state-of-the-art technologies such as CRISPR/Cas9 knock out or in vitro selection of RNA binding motifs (bind’n’seq). We also started to investigate novel RNA binding proteins and RNA binding domains (see 3).

Finally, we characterize specific modifications on RNA molecules. The availability of antibodies against m6Adenin (m6A) allowed for a better characterization of this modification. Interestingly, this modification is highly abundant on mRNAs and many interesting biological functions of this modification have been reported. In our projects, we characterize enzymes and RNA binding proteins that act in this modification pathway. In addition, we generate monoclonal antibodies against a set of ten different base modifications. With these tools, we hope to map such modifications on RNA molecules and generate a dynamic view on the biology of RNA base modifications (see 4).