Genomic views of protein-RNA interactions and splicing regulation

Posttranscriptional regulation plays a critical role in development and tissue identity. The information in the RNA sequence and how it is read and interpreted by RNA-binding proteins is commonly referred to as the ‘ribonucleoprotein (RNP) code’. Cracking this code and understanding the underlying regulatory networks remain long-standing goals of RNA biologists.

To decipher the RNP code, I previously developed iCLIP, a technique that provides genome-wide maps of protein-RNA interactions with single-nucleotide resolution. Our group uses iCLIP to address the following key questions: What is the organisation of cis-regulatory elements? How do proteins act together in RNP assembly? How do RNPs control gene regulation in early development? By cracking the RNP code, we aim to better understand human biology and disease.

Research website

Positions held

  • Since 2013: Group Leader, Institute of Molecular Biology (IMB), Mainz
  • 2008 - 2013: Postdoctoral Researcher, MRC Laboratory of Molecular Biology, Cambridge


  • 2008: PhD in Biology, Phillip University, Marburg
  • 2003: Diploma in Biology, Ludwig Maximilian University, Munich

Selected publications by Julian König

Kang HS*, Sánchez-Rico C*, Ebersberger S, Sutandy FXR, Busch A, Welte T, Stehle R, Hipp C, Schulz L, Buchbender A, Zarnack K, König J# and Sattler M# (2020) An autoinhibitory intramolecular interaction proof-reads RNA recognition by the essential splicing factor U2AF2Proc Natl Acad Sci, 117:7140–7149 (*indicates joint contribution, #indicates joint correspondence) Link

Buchbender A, Mutter H, FX Sutandy R, Körtel N, Hänel H, Busch A, Ebersberger S and König J (2019) Improved library preparation with the new iCLIP2 protocolMethods, doi:10.1016/j.ymeth.2019.10.003 Link

Braun S*, Enculescu M*, Setty ST*, Cortés-López M, de Almeida BP, Sutandy FXR, Schulz L, Busch A, Seiler M, Ebersberger S, Barbosa-Morais NL, Legewie S#, König J# and Zarnack K# (2018) Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesisNat Commun, 9:3315 (*indicates joint contribution, #indicates joint correspondence) Link

Hildebrandt A, Alanis-Lobato G, Voigt A, Zarnack K, Andrade-Navarro MA, Beli P and König J (2017) Interaction profiling of RNA-binding ubiquitin ligases reveals a link between posttranscriptional regulation and the ubiquitin systemSci Rep, 7:16582 Link

König J, Zarnack K, Luscombe NM and Ule J (2012) Protein–RNA interactions: New genomic technologies and perspectivesNat Rev Genet, 13:77–83 Link