Stefan Stamm

Research Focus

We are studying alternative splicing in mammalian systems. We identified novel regulatory factors, determined how splice site selection is regulated by external stimuli and generated databases of alternative exons.

For the analysis of splicing factors, we pioneered and established in vivo splicing assays that rely on cotransfection of reporter minigenes and splicing factors. Using these in vivo systems, we could demonstrate that alternative splice site selection is influenced by reversible phosphorylation events, which explains the frequently observed changes of alternative splicing during development or tumorigenisis. Using tau exon 10 and SMN2 exon 7 as models for neurodegenerative diseases, we proved the concept that missplicing events observed in several diseases can be reversed in vivo.

Recently, we could show that small RNAs, like the snoRNA HBII-52 can regulate alternative splice site selection. To study the genome-wide relevance and regulation of alternative splicing, we developed databases of alternative exons. These databases rely on high quality curated data obtained from the literature. The databases have been merged with datasets derived from computational pipelines and are now hosted at the European Bioinformatics Center. Included in the databases are now published regulatory sequences and functions of alternative exons.

Publications

1. Stamm, S. (2008). Regulation of alternative splicing by reversible phosphorylation. Journal of Biological Chemistry 283(3), 1223-7.
2. Novoyatleva, T., Heinrich, B., Tang, Y., Benderska, N., Butchbach, M.E., Lorson, C.L., Lorson, M.A., Ben-Dov, C., Fehlbaum, P., Bracco, L., Bollen, M. and Stamm, S. (2008). Protein phosphatase 1 binds to the RNA recognition motif of several splicing factors and regulates alternative pre-mRNA processing. Human Molecular Genetics 17(1), 52-70.
3. Hiller, M., Zhang, Z., Backofen, R. and Stamm, S. (2007). pre-mRNA secondary structure and splice site selection. PLOS Genetics 3(11), 2147-2155.
4. Kishore, S., and Stamm, S. (2006). The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science 311, 230-232.
5. Stamm, S., Riethoven, J.J., Le Texier, V., Gopalakrishnan, C., Kumanduri, V., Tang, Y., Barbosa-Morais, N.L. and Thanaraj, T.A. (2006). ASD: a bioinformatics resource on alternative splicing. Nucleic Acids Research 34, D46-55.

Key lab techniques: in vivo minigene analysis, two hybrid screening, reporter gene construction, protein:protein interaction, gateway system, Alzheimer Disease, spinal muscular atrophy, Prader-Willi-Syndrome.

Key lab reagents: gateway clones, expression cDNAs, tra2-beta1 antisera.

Lab contact: Stefan Stamm: stefan@stamms-lab.net

Lab website: www.stamms-lab.net