Our group is interested in the investigation of protein–RNA interactions. We focus especially on the development of novel analytical techniques that enable us to identify hitherto unknown proteins in direct contact with RNA after UV cross-linking of native ribonucleoprotein (RNP) particles.
For the detection, determination and identification of spliceosomal proteins we are currently establishing new, improved and increasingly sensitive mass-spectrometric methods (MALDI and ESI) combined with chromatographic enrichment strategies. Recently, we succeeded in sequencing both the peptide and the RNA parts of isolated RNP cross-links solely by MALDI and ESI. The extremely low quantity of material needed for such analyses paves the way for the investigation of RNP complexes present in low abundance.
Our protein-analytical strategies and mass-spectrometric technologies are further applied to the study of post-translationally modified proteins in protein–RNA complexes and, importantly, for the elucidation of the stoichiometries and quantities of protein factors, especially those involved in alternative splicing.
- Palfi, Z., Jaé, N., Preusser, C., Kaminska, K.H., Bujnicki, J.M., Lee, J.H., Günzl, A., Kambach, C., Urlaub, H., Bindereif, A. (2009) SMN-assisted assembly of snRNP-specific Sm cores in trypanosomes. Genes and Development 23(14), 1650-64.
- Weinmann, L., Höck, J., Ivacevic, T., Ohrt, T., Mütze, J., Schwille, P., Kremmer, E., Benes, V., Urlaub, H., Meister, G. (2009) Importin 8 Is a Gene Silencing Factor that Targets Argonaute Proteins to Distinct mRNAs. Cell 136(3), 496-507.
- Mathew, R., Hartmuth, K., Möhlmann, S., Urlaub, H., Ficner, R., Lührmann, R. (2008) Phosphorylation of human PRP28 by SRPK2 is required for integration of the U4/U6-U5 tri-snRNP into the spliceosome. Nature Structural and Molecular Biology 15(5), 435-43.
- Mukherjee, K., Sharma, M., Urlaub, H., Bourenkov, G.P., Jahn, R., Südhof, T.C., Wahl, M.C. (2008) CASK Functions as a Mg2+-independent neurexin kinase. Cell 133(2), 328-39.
- Bessonov, S., Anokhina, M., Will, C.L., Urlaub, H., Lührmann, R. (2008) Isolation of an active step I spliceosome and composition of its RNP core. Nature 452(7189), 846-50.
- Martin, N., Schwamborn, K., Urlaub, H., Gan, B., Guan, J.L., Dejean, A. (2008) Spatial interplay between PIASy and FIP200 in the regulation of signal transduction and transcriptional activity. Molecular and Cellular Biology 28(8), 2771-81.
- Kühn-Hölsken, E., Dybkov, O., Sander, B., Lührmann, R., and Urlaub, H. (2007) Improved identification of enriched peptide RNA cross-links from ribonucleoprotein particles (RNPs) by mass spectrometry. Nucleic Acids Research 35, e95.
- Karaduman, R., Fabrizio, P., Hartmuth, K., Urlaub, H., Luhrmann, R. (2006) RNA Structure and RNA-Protein Interactions in Purified Yeast U6 snRNPs. Journal of Molecular Biology 356, 1248-62.
- Kühn-Hölsken E., Lenz C., Sander B., Lührmann R. & Urlaub H. (2005) Complete MALDI-ToF analysis of cross-linked peptide–RNA oligonucleotied derived from nonlabled UV-irradiated ribonucleoprotein particles. RNA 11, 1915-30.
- Zalfa F., Adinolfi S., Napoli J., Kühn-Hölsken E., Urlaub H., Achsel T., Pastore A. and Bagni C. (2005) Fragile X mental retardation (FMRP) binds specifically to the brain cytoplasmic RNAs BC1/BC200 via a novel RNA-binding motif. Journal of Biological Chemistry 280, 33403–33410.
- Rhode, B.M., Hartmuth, K., Urlaub, H. and Lührmann, R. (2003) Analysis of site-specific protein–RNA cross-links in isolated RNP complexes, combining affinity selection and mass spectrometry. RNA 9, 1542–1551.
- Nottrott, S., Urlaub, H. and Lührmann, R. (2002) Hierarchical, clustered protein interactions with U4/U6 snRNA: a biochemical role for U4/U6 proteins. EMBO Journal 21, 5527–38.
- Urlaub, H., Hartmuth, K. and Lührmann, R. (2002) A two-tracked approach to analyze RNA–protein crosslinking sites in native, nonlabeled small nuclear ribonucleoprotein particles. Methods, 26, 170–81.
- Urlaub, H., Raker, V.A., Kostka, S. and Lührmann, R. (2001) Sm protein-Sm site RNA interactions within the inner ring of the spliceosomal snRNP core structure. EMBO J, 20, 187–96.
- Urlaub, H., Hartmuth, K., Kostka, S., Grelle, G. and Lührmann, R. (2000) A general approach for identification of RNA–protein cross-linking sites within native human spliceosomal small nuclear ribonucleoproteins (snRNPs). Analysis of RNA–protein contacts in native U1 and U4/U6.U5 snRNPs. Journal of Biological Chemistry 275, 41458–68.
Key lab techniques: tRNA endonucleases; mouse mutagenesis; Cre-lox technology; Archaeaexpress; GPR 37 expression; Parkinson Disease.
Key lab reagents: Mouse mutants; EMMA collection.
Lab contact: Marcello Raspa: email@example.com