Seminar: Ivo Hofacker

5'UTR Structure and its Role in Transcription and Translation

2017-11-17: Ivo Hofacker, TBI, University of Vienna. The seminar will take place November 17, 13.30-14.15 at University of Copenhagen, SUND/SCIENCE, Building 1-04, Grønnegårdsvej 7, 1st floor library, Frederiksberg C.


Both Transcription and Translation of prokaryotic mRNAs are heavily influenced by the RNA structures formed by their 5'UTR. Many mRNAs carry potential "terminator hairpins" upstream of the start codon that can cause the polymerase to terminate transcription and thus shut-off gene expression. In order to be effective, terminator hairpins have to form immediately after being transcribed. The effect is therefore dependent on the kinetics of co-transcriptional folding. As an example, I will present computational modeling of a purine riboswitch where the terminator hairpin is always thermodynamically stable, but only in the presence of the ligand it is formed fast enough to cause termination.

Translation initiation in prokaryotes is driven by RNA-RNA interaction between the mRNA and the ribosomal RNA, and therefore competes with intramolecular mRNA structure. Indeed, bacterial mRNAs are remarkably weakly structured around the ribosome binding site. This is in contrast to eukaryotic genes, which are much more structured. Presumably this is one reason, why human genes are often poorly translated in a prokaryotic systems. I will present models for the translation initiation efficiency and demonstrate how these can be used to predict the effect of small RNA regulation, but also to optimize eukaryotic mRNA sequences for efficient expression in prokaryotes.

The seminar is arranged by the NextProd consortium in collaboration with the Danish RNA society and the Center for non-coding RNA in Technology and Health.