An RNA story, from chromatin to protein

Abstract

RNA functions expand well over just coding for protein effectors. Non-coding RNAs oversee translation, RNA processing, and spatial organization of the cellular space, therefore participating in the regulation of almost any cellular process. To add a further layer of complexity, both coding and non-coding RNAs are extensively modified. These modifications determine RNA stability and localization, often by changing the way the single RNA molecules interact with RNA-binding proteins.

In paper I, we describe how RNA contributes to maintaining an open chromatin structure by neutralizing the positive charge on the histone-tails. This effect, which seems to depend only on the charge of the RNA molecule, is not mediated by newly transcribed RNAs, but rather on RNA species that are stable in time, and possibly coincide with LINE- 1 containing transcripts.

In paper II, we explore the role of dyskerin, the only RNA-guided pseudouridine synthase expressed by human cells, in mediating co-transcriptional modification of mRNAs, which in turn regulates their translation. Dyskerin travels along RNA polymerase II over transcribed genes, and binds – possibly modifying – thousands of mRNAs. After a shortterm depletion of dyskerin, pseudouridylation levels on mRNAs drop dramatically, and translation levels show an overall increase. We show that this effect depends on the enzymatic function of dyskerin and that pseudouridine directly inhibits translation in vitro. Conversely, we find that prolonged removal of dyskerin results in an overall drop in translational rates, and that this is linked to rRNA processing defects caused by long-term depletion of dyskerin. Our results also reveal that mRNA pseudouridylation is reduced in cells from dyskeratosis congenita patients, where dyskerin is impaired, therefore offer novel insight on the molecular mechanism behind this syndrome.

In paper III, we investigate the role of mRNA pseudouridylation in the heat-shock response, focusing on the formation of stress granules. Pseudouridine levels increase after heat-shock, and removal of three different enzymes involved in mRNA pseudouridylation results in defective stress granule formation. Hypo-pseudouridylated mRNAs accumulate within stress granules, and translation recovery after stress is impaired.

Taken together, these results expand on the multi-faceted role of RNA and RNA modification in regulating multiple fundamental cellular processes. The insight they offer on the inner workings of human cells and the molecular mechanism behind dyskeratosis congenita will hopefully contribute to the identification of novel therapeutic targets for dyskeratosis congenita and other diseases.