Research update: evolutionary conserved RNA-binding proteins

During the last years, hundreds of novel RNA-binding proteins (RBPs) have been detected in mammalian cell lines. Now, we mapped the mRNA-bound proteome of a complete organism: the yeast S. cerevisiae. Additionally, we determined the mRNA interactome of human hepatocytic cells (HuH-7).

Having comprehensive information on RBPs from a eukaryotic single cell organism and from mammalian cell lines, we defined a conserved core mRNA interactome of eukaryotic mRNA-binders. The core consists of many well-established RNA-binding proteins but also of many enzymes from diverse biochemical pathways and glycolysis emerges as hot-spot of conserved RBPs.

We also identified another interesting difference among some conserved eukaryotic RBPs in their overall RNA-binding architecture: throughout evolution, a steady increase in the repetition of short amino acid tripeptide motifs in unstructured regions of proteins could be observed.


Beckmann BM, Horos R, Fischer B, Castello A, Eichelbaum K, Alleaume A-M, Schwarzl T, Curk T, Foehr S, Huber W, Krijgsveld J & Hentze MW.  The RNA-binding proteomes from yeast to man harbour conserved enigmRBPs. Nature Communications (2015); 6:10127


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.



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