Gene silencing by RNAi and DNA Methylation

• Antragsteller: Professor Dr. Wolfgang Nellen
• Fachliche Zuordnung: Allgemeine Genetik und funktionelle Genomforschung
• Förderung: Förderung von 2002 bis 2009
• Projektkennung: Deutsche Forschungsgemeinschaft (DFG) - Projektnummer 5370384

• Erstellungsjahr: 2009

Zusammenfassung der Projektergebnisse

This project in the SPP was subdivided into two main topics: the elucidation of RNAi pathways in Dictyostelium and epigenetic effects on the genetic material i.e. DNA and chromatin modification. We have shown RNAi function in Dictyostelium and identified most of the key players in this organism. With the putative RNA helicase HelF we identified a new component that serves as a negative regulator of RNAi. In collaboration with the Söderbom group (Upsalla) we found that the majority of endogenous SiRNAs was derived from the centromeric retroelement DIRS-1 that was also subject to DNA methylation. DnmA, a homolog of Dnmt2 was identified as the enzyme responsible for the weak DNA methylation in Dictyostelium. Related to DNA methylation, we invesfigated epigenetic marks in chromatin remodelling, histone modifications and histone associated proteins.

Projektbezogene Publikationen (Auswahl)

• (2004): A database search for double-strand containing RNAs in Dictyostelium discoideum. Biological Chemistry 385, 961-965
  S. Graf, B. E. Borisova, W. Nellen, G. Steger & C. Hammann
  
• (2004): Novel thioredoxin targets in Dictyostelium discoideum identified by two-hybrid analysis. Interactions of thioredoxin with elongation factor lo and yeast alcohol dehydrogenase. Biological Chemistry, 385, 1185-1192
  T. Brodegger, A. Stockmann, J. Oberstraß, W. Nellen, and H. Follmann
  
• (2005): Hammerhead ribozymes encoded in the genome of A. thaliana. Plant Cell 17, 1877-1885
  R. Przybilski, S. Graf, A. Lescoute-Phillips, E. Westhof, W. Nellen, G. Steger, C. Hammann
  
• (2005): Silencing of retrotransposons in Dictyostelium by DNA methylation and RNAi. Nucleic Acids Res. 33, 6405-6417
  M. Kuhlmann, B. E. Borisova, M. Kaller. P. Larsson, D. Stach, J. Na, L. Eichinger, F. Lyko, V. Ambros, F. Söderbom, C. Hammann and W. Nellen
  (Siehe online unter https://doi.org/10.1093/nar/gki952)
• (2006): Developmental Timing in Dictyostelium is Regulated by the Set1 Histone Methyltransferase. Dev. Biol., 292, 519-532
  J. R. Chubb, G. Bloomfield, Q. Xu, M. Kaller, A. Ivens, J. Skeöton, B. Turner, W. Nellen, G. Shaulsky, R. R. Kay, W. A. Bickmore, R. H. Singer
  
• (2006): HelF, a putative RNA helicase acts as a nuclear suppressor of RNAi but not antisense mediated gene silencing. Nucleic Acids Res., 34, 773-784
  B. Popova, M. Kuhlmann, A. Hinas, F. Söderbom & W. Nellen
  (Siehe online unter https://doi.org/10.1093/nar/gkj465)
• (2006): Non-redundant HPI-like proteins in Dictyostelium discoideum: different functions during vegetative growth. Eukaryotic Cell 5, 530-543
  M. Kaller, U. Euteneuer & W. Nellen
  
• (2007): Mitotic localisation of protein factors involved in chromosome inheritance in Dictyostelium discoideum. Biological Chemistry, 388, 355-365
  M. Kaller, B. Földesi & W. Nellen
  
• (2007): The M.EcoRV DNA-(adenine N6)-methyltransferase uses direct readout and indirect readout for DNA recognition. J. Biol. Chem. 282, 36942-52
  T. P. Jurkowski, N. Anspach, L. Kulishova, W. Nellen & A. Jeltsch
  
• (2007): The small RNA repertoire of Dictyostelium discoideum and its regulation by components of the RNAi pathway. Nucleic Acids Res. 35, 6714-26
  A. Hinas, J. Reimegard, E.G.H Wagner, W. Nellen, V. Ambros F. Söderi^om
  
• (2008) Human DNMT2 methylates tRNA(Asp) molecules using a DNA methyltransferase-like catalytic mechanism. Rna, 14, 1663-1670
  Jurkowski, T.P., Meusburger, M., Phaike, S., Helm, M., Nellen, W., Reuter, G. and Jeltsch, A.
  
• (2008): Dictyostelium Aurora kinase has properties of both Aurora A and Aurora B kinases. Eukaryotic Cell, 7, 894-905
  Li, H., Chen, Q., Kaller, M., Nellen, W., Graf, R. and De Lozanne, A.
  
• (2008): Nanocrystalline diamond/amorphous carbon composite coatings for biomedical applications. Diamond & Related Materials 17 (2008) 882-887
  Popov, C, Bliznakov, S., Boycheva, S., Milinovik, N., Apostolova, M.D., Anspach, N., Hammann, C., Nellen, W., Reithmaier, J.P. and Kulisch, W.
  
• (2008): Structure and function of Dnmt3a and Dnmt3/3L nucleoprotein filaments. Nucleic Acids Res. 36(21), 6656-6663
  Jurkowska, R.Z., Ragozine, S., Ansbach, N., Urbanke, C., Nellen, W., Cheng, X. and Jeltsch, A.
  
• (2009): Histone deacetylases regulate multicellular development of the social amoeba Dictyostelium discoideum. J. Mol. Biol. 391, 833-848
  Sawarkar, R., Visweswariah, S. S., Nellen, W. and Nanjundiah, V.