Understanding how RNA-binding proteins (RBPs) determine the splicing outcome is fundamental to human biology and disease. Splicing is regulated by activators and repressors that recognise cis-elements at their target exons. However, it is clear that RBP recruitment is not solely dependent on the underlying RNA sequence, but is strongly shaped by the interactive environment. Means of interaction include the direct competition or cooperative recruitment of RBPs as well as modulations of secondary structure. However, the general rules that govern the interactive assembly of pre-messenger ribonucleoprotein (pre-mRNP) complexes remain to be established. Our lab unites a systemic picture of pre-mRNP assembly during splicing with the molecular understanding of the underlying processes. We employ cutting-edge genomic RNA biology techniques, such as iCLIP and RNA-seq, in combination with biochemical and genetic tools. An important aspect of our work is the computational analysis and integration of our genome-wide data sets, and we closely collaborate with bioinformatics experts.
Key techniques: iCLIP, RNAseq, Minigenes, etc.
Research system/organism: Mammalian cell culture
- K. Zarnack*, J. König*, M. Tajnik, I. Martincorena, S. Eustermann, I. Stévant, A. Reyes, S. Anders, NM. Luscombe, J. Ule (2013) Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements. Cell 152: 453-466
- J. König*, K. Zarnack*, G. Rot, T. Curk, M. Kayikci, B. Zupan, DJ. Turner, NM. Luscombe, J. Ule (2010) iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol 17: 909-915
- J. König, K. Zarnack, N.M. Luscombe, J. Ule (2012) Protein-RNA interactions: new genomic technologies and perspectives. Nat Rev Genet 13: 77-83
- Y. Sugimoto, J. König, S. Hussain, B. Zupan, T. Curk, M. Frye, J. Ule (2012) Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions. Genome Biol 13(8):R67 [Epub ahead of print]
- J. König, K. Zarnack, G. Rot, T. Curk, M. Kayikci, B. Zupan, DJ. Turner, NM. Luscombe, J. Ule (2011) iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution. J Vis Exp DOI: 10.3791/2638