Research update: Mapping RNA-binding sites in proteins

Understanding RNA-protein interactions requires researchers to investigate both binding partners: RNA and RNA-binding proteins (RBPs). Unfortunately, methods to study both molecules are differentially well developed. Whereas new high-throughput techniques for RNA research such as PAR-CLIP or iCLIP allow to pinpoint protein binding sites in RNA at nucleotide resolution for millions of sequences, we so far could not do the complementary experiment: mapping interaction sites of RNA within proteins in an unbiased and high throughput fashion.

Participating in a study from Henning Urlaubs lab (MPI Göttingen, Germany), we could now develop a mass-spectrometry-based technique that maps more than 250 RNA interactions in 124 proteins: RNPxl. The method was tested in human and yeast cells and allows to identify those amino acids in RBPs which were interacting with RNA.

 

Literature:

Kramer K, Sachsenberg T, Beckmann BM, Qamar S, Boon K-L, Hentze MW, Kohlbacher O & Urlaub H. Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteinsNature Methods (2014); 11(10):1064-1070