Project 462393

It has been reported by the Encyclopedia of DNA Elements (ENCODE) and the Functional Annotation of Mouse (FANTOM) consortiums that coding transcripts represent less than 3% of the total genome. These findings surprisingly suggest that the majority of transcription products have no coding potential. It was traditionally considered that the existence of such non-coding transcripts represented "transcriptional noise" coming from "junk DNA", but recent work suggests that a significant portion of non-coding transcripts are functionally active RNA molecules. It is expected that such non-coding RNAs primarily exert their biological function by their structure and their interaction with cellular partners. Non-coding transcripts are exemplified by riboswitches, which are structured elements typically found in the 5' untranslated regions of mRNAs. Riboswitches regulate gene expression by altering their structure upon binding to small cellular metabolites. Similarly to the majority of non-coding RNAs, very little information is known regarding how the structure of riboswitches is used to modulate genetic expression. As a result, it is imperative to employ novel high-resolution methods to characterize RNA structures under conditions closer to the in vivo context, most preferably allowing to study the structure of nascent transcripts. A major goal of our research is to unravel the molecular mechanisms by which riboswitches perform ligand binding during their transcription (i.e., co-transcriptionally) to control gene expression. Our research could be used to design novel single-molecule tools assessing antimicrobial drugs targeting riboswitches in a cotranscriptional context. We also plan to study the structures of human nascent transcripts using a novel assay. The knowledge obtained from this research will also be generally applicable to study more complex systems, such as RNA viruses and long-coding RNAs associated to cardiovascular diseases and several types of cancer.