RNA folding and catalysis, RNA-binding antibiotics

Meanwhile everybody knows what DNA, desoxyribonucleic acid, means. In contrast, RNA, ribonucleic acid, has attracted little attention although is fulfils significantly more tasks in the cell than DNA. RNA is able to store genetic information, (genetic material of HIV and influenza viruses consists of RNA) and like proteins RNA is able to promote specialised cellular reactions. The aim of my research group is to understand how functional RNA molecules achieve their activities. RNA molecules are composed of long chains, which have to fold into complex three-dimensional structures to reach an active state. The main research project in my group aims at understanding the fundamental rules, which govern this folding process and what is done to avoid misfolding of RNA molecules. Our observation that some antibiotics bind to RNA and inhibit its function was central to the notion that RNA molecules are targets for therapeutical interventions. We are interested to know how antibiotics bind to RNA and how they modulate its function.

One of the big surprises revealed by the sequencing of whole genomes, was the high content of repeat sequences, which were quickly declared as "genomic junk". A few years later, when efforts were made to sequence RNA to find out which parts of the genome are transcribed, the surprise was even bigger: a large portion of the genome is transcribed into RNA, even the junk. Because the plasticity of the genome is mainly due to retroelements (RNAs which are reverse transcribed and inserted into the genome), I am convinced that the genomic junk is mainly derived from functional RNAs, per se interesting and worth trying to discover its function. I therefor devoted a large part of the Wittgenstein award trying to analyse the genomic junk. The discovery of new genes is most often attempted via genetic screens, bioinformatic predictions or sequencing of RNA. To address the function of the genomic junk, a completely different approach was necessary because its mutation most probably does not have a phenotype, we cannot predict unknown things and because it is mostly silence, sequencing RNA would not have been possible. We took a different approach: we used genomic SELEX, a technique which starts by constructing libraries derived from genomic DNA and transcribing it into RNA in vitro. Then these libraries are screened for diverse functions. We selected for RNAs with high affinity to RNA polymerases and to the bacterial RNA chaperone Hfq. We call the RNA sequences that we discovered "genomic aptamers". We isolated a very high number of aptamers from antisense strands and from satellite repeats mappig to centromers. We are currently analysing the function of these aptamers, which seem to be involved in transcriptional silencing. Many RNAs have as function to silence genomic regions at several levels of gene expression. We made substantial progress in understanding how RNAs anneal to their target sequences with the help of proteins with RNA annealing activity. In summary, we have adapted the classical SELEX approach to be used in combiantion with genome sequences and deep sequencing to discover novel features of RNA molecules in silenced regions of genomes.