Nascent Epitranscriptomics - Insights into RNA processing

Abstract

The current thesis studies the RNA processing dynamics in a high-resolution time scale manner. The method used, called BrU Chase Seq, determined the processing kinetics of pri-miRNAs within intact cells over time using a pulse-chase approach to obtain nascent RNA within a 1-hour window after transcription. Further analysis showed that primiRNAs exhibit different processing kinetics ranging from fast over intermediate to slow processing. In addition, polycistronic pri-miRNAs show differential processing. The second part of the thesis describes for the first time the role of m6A RNA modification impact on RNA splicing kinetics. Two techniques have been developed namely TNT-Seq and qTNT-Chase Seq. These techniques provide the first time-resolved high-resolution assessment of m6A on nascent RNA transcripts and unveil its importance for the control of RNA splicing kinetics. More specifically, the early co-transcriptional m6A deposition near splice junctions promotes fast splicing, while m6A modifications in introns are associated with long, slowly processed introns and alternative splicing events. In conclusion, the early m6A deposition specifies the fate of transcripts regarding splicing kinetics and alternative splicing.