Partner group of Max Planck Institute for Molecular Cell Biology and Genetics (MPI-CBG)
Research topics
RNA molecules are not just messengers acting between DNA and proteins but rather required factors that play an active role in the expression of genes encoded in our genome. An RNA processing step called splicing can dramatically increase the diversity of proteins in human cells and tissues. RNA splicing is catalyzed by a large macromolecular complex, the spliceosome, which is formed from several RNA-protein complexes called snRNPs. In our group we are interested in spliceosome assembly, the organization of RNA splicing in the cell nucleus and regulation of alternative splicing. We also aim to determine how mutations in splicing factors can cause retinitis pigmentosa, a human genetic disease characterized by photoreceptor cell degeneration.
Using advanced microscopy techniques (e.g. live cell imaging, FRET, FCS) we explore where and when the spliceosome assembles in the cell nucleus. Experimental data are then used for modelling of spliceosome assembly in the 3D space of the nuclear landscape. We identified the conserved nuclear compartment, the Cajal body, as the site of snRNP assembly and recycling, and proposed a model stating that the presence of Cajal bodies increases the efficiency of snRNP formation.
Assembly of the spliceosome in vivo. Currently, it is unknown how splicing machinery assembles in the cell nucleus. To analyze spliceosome assembly in situ we created a battery of stable cell lines expressing splicing factors tagged with fluorescent proteins. These cells are used for measurements of interactions and dynamics of individual proteins directly in living cells.
Current Grant Support
GACR grant no.: GA204/07/0133; 2007-2011: Self-organization principles of non-membrane-bound organels in eukaryotic cells. (collaboration with Jan Malínský from IEM AS CR)
MPI-partner group 2006-2010: Pre-mRNA splicing and organization of the cell nucleus.
AS CR project KAN200520801 - Targeted expression and transport of bioactive molecules
Most important recent papers
(2003-present; names of the lab members underlined)Stanek, D., Rader, S.D., Klingauf, M., & Neugebauer, K.M. (2003) Targeting of U4/U6 small nuclear RNP assembly factor SART3/p110 to Cajal Bodies. J. Cell Biol. 160:505-516, 2003. (PubMed) (FullText)
Dundr. M, Hebert, M.D., Karpova, T.S., Stanek, D., Xu, H., Shpargel, K.B., Meier, T.U., Neugebauer, K.M., Matera, A.G., Misteli, T.: In vivo kinetics of Cajal body components. J. Cell Biol. 164:831-842, 2004. (PubMed) (FullText)
Stanek, D., Neugebauer, K.M.: Detection of snRNP assembly intermediates in Cajal bodies by FRET. J. Cell Biol. 166:1015-25, 2004. (PubMed) (FullText)
Klingauf M., Stanek, D., Neugebauer KM.: Enhancement of U4/U6 small nuclear ribonucleoprotein particle association in Cajal bodies predicted by mathematical modeling. Mol. Biol. Cell 17:4972-81, 2006. (PubMed) (FullText)
Cvackova. Z., Albring, K.F., Koberna. K., Ligasova, A., Huber, O., Raska, I., Stanek, D. (2008) Pontin is localized in nucleolar fibrillar centers. Chromosoma 117:487-97. (PubMed) (FullText)
Stanek, D., Pridalova-Hnilicova, J., Novotny, I., Huranova, M., Blazikova, M., Wen, X., Sapra, A.K., Neugebauer, K.M. (2008) Spliceosomal small nuclear ribonucleoprotein particles repeatedly cycle through Cajal bodies. Mol. Biol. Cell 19:2534-43. (PubMed) (FullText)
Cvackova Z, Masata M, Stanek D, Fidlerova H, Raska I. (2009) Chromatin position in human HepG2 cells: Although being non-random, significantly changed in daughter cells. J Struct Biol. 165:107-17. (PubMed)
Huranova M, Hnilicova J, Fleischer B, Cvacková Z, Stanek D. (2009) A mutation linked to retinitis pigmentosa in HPRP31 causes protein instability and impairs its interactions with spliceosomal snRNPs. Hum Mol Genet. 18:2014-23. (PubMed)
Huranova M, Jablonski JA, Benda A, Hof M, Stanek D, Caputi M (2009) In vivo detection of RNA-binding protein interactions with cognate RNA sequences by fluorescence resonance energy transfer. RNA (in press)
Reviews
Neugebauer, K.M., Geiger, J.A., Kotovic K.M., Stanek, D.: Pre-mRNA processing in the nuclear landscape. In Visions of the Cell Nucleus - Eukaryotic DNA. P. Hemmerich and S. Diekmann, eds. American Scientific Publishers. 36 pages.
Stanek, D., Neugebauer, KM.: The Cajal body: a meeting place for spliceosomal snRNPs in the nuclear maze. Chromosoma. 115:343-54, 2006. (PubMed) (FullText)
Teaching, lectures, public presentations
MB150P91E - RNA structure and function - download presentations (password protected access)
Staněk D. (2009) Překvapivá souvislost - degenerace oční sítnice a pre-mRNA sestřih. Akademický bulletin 09/2009 (PDF).