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.
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 proteins. Nature Methods (2014); 11(10):1064-1070