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AG Kilchert



The 3’ to 5’ exonucleolytic RNA exosome complex is a major regulator of RNA stability in the cell and degrades many types of RNA substrates. The complex is essential in all eukaryotes and exosome dysfunction has been linked to cancer and disease. While the molecular function and the structure of the complex are very well understood, the factors that determine substrate selectivity and allow regulation of its activity remain largely obscure. We ask: What factors are involved in exosome targeting? How is substrate selection regulated ins response to external cues? How does targeted RNA decay contribute to resilience towards stress? Using the fission yeast Schizosaccharomyces pombe as a model organism, we aim to identify RNA-binding proteins that direct RNA substrates towards the exosome, to discover their mode of substrate recognition, and analyse their exosome targeting capacity in vivo and in vitro.


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We explore mechanisms of post-transcriptional gene regulation and use molecular biology and biochemical methods to study the regulation of RNA decay in the cell nucleus, with a particular focus on the cellular response to DNA damage. Among others, we employ RNA-protein crosslinking and high-throughput sequencing techniques. We welcome applications from Master students, PhD students, and postdocs with a keen interest in RNA biology, and offer a highly motivated environment with excellent conditions for scientific training. For further information or applications please contact Dr. Cornelia Kilchert.





  •  Birot, A., Kus, K., Priest, E., Alwash, A. Al, Castello, A., Mohammed, S., Vasiljeva, L. and Kilchert, C. (2021) RNA-binding protein Mub1 and the nuclear RNA exosome act to fine-tune environmental stress response. Life Sci. Alliance, 5, e202101111.

  • Kilchert, C., Kecman, T., Priest, E., Hester, S., Aydin, E., Kus, K., Rossbach, O., Castello, A., Mohammed, S., Vasiljeva, L. (2020) “System-wide analyses of the fission yeast poly(A)+RNA interactome reveal insights into organization and function of RNA-protein complexes.” Genome Res. 30(7):1012–1026.
  • Kilchert, C. (2020) “RNA exosomes and their co-factors.” Methods Mol Biol. 2062:215-235.
  • Kilchert, C. Hester, S., Castello, A., Mohammed, S., Vasiljeva, L. (2020) “Comparative poly(A)+ RNA interactome capture of RNA surveillance mutants.” Methods Mol Biol. 2062:255-276.
  • Kilchert, C., Sträßer, K., Kunetsky, V., Änkö, M.L. (2019) “From parts lists to functional significance—RNA–protein interactions in gene regulation.” Wiley Interdiscip Rev RNA:e1582. - Review
  • Watts, B.R., Wittmann, S., Wery, M., Gautier, C., Kus, K., Birot, A., Heo, D.H., Kilchert, C., Morillon, A., Vasiljeva, L. (2018) “Histone deacetylation promotes transcriptional silencing at facultative heterochromatin.” Nucleic Acids Res. 46(11):5426-5440.
  • Wittmann, S., Renner, M., Watts, B., Adams, O., Huseyin, M., Baejen, C., El Omari, Kilchert, C., Heo, D.H., Kecman, T., Cramer, P., Grimes, J., Vasiljeva, L. (2017) “The conserved protein Seb1 drives transcription termination by binding RNA polymerase II and nascent RNA” Nat Commun. 8:14861.
  • Kilchert, C., Wittmann, S., Vasiljeva, L. (2016) “The regulation and functions of the nuclear RNA exosome complex” Nat Rev Mol Cell Biol. 17(4):227-39. - Review
  • Kilchert, C., Wittmann, S., Passoni, M., Shah, S., Granneman,. S., Vasiljeva, L. (2015) “Regulation of mRNA Levels by Decay-Promoting Introns that Recruit the Exosome Specificity Factor Mmi1” Cell Rep. 13(11):2504-15.
  • Shah, S., Wittmann, S.*, Kilchert, C.*, Vasiljeva, L. (2014) “lncRNA recruits RNAi and the exosome to dynamically regulate pho1 expression in response to phosphate levels in fission yeast” Genes Dev. 28(3):231-44. *These authors contributed equally
  • Kilchert, C., Vasiljeva, L. (2013) “mRNA quality control goes transcriptional” Biochem Soc Trans. 41(6):1666-72. - Review
  • Volanakis, A., Passoni, M., Hector R.D., Shah, S., Kilchert, C., Granneman, S., Vasiljeva, L. (2013) “Spliceosome-mediated decay (SMD) regulates expression of nonintronic genes in budding yeast” Genes Dev. 27(18):2025-38.
  • Kilchert, C., Spang, A. (2011) „ Cotranslational transport of ABP140 mRNA to the distal pole of S. cerevisiae.EMBO J. 30(17):3567-80.
  • Kilchert, C., Weidner, J., Prescianotto-Baschong, C., Spang, A. (2010) „Defects in the secretory pathway and high Ca2+ induce multiple P-bodies.” Mol Biol Cell. 21(15):2624-38.
  • Kamena, F., Diefenbacher, M., Kilchert, C., Schwarz, H., Spang, A. (2008) „Ypt1p is essential for retrograde Golgi-ER transport and for Golgi maintenance in S. cerevisiae.” J. Cell Sci. 121(8):1293-302.