Project Outline

Accurate gene expression is crucial for the survival of all life forms. RNA helicases are a large class of enzymes involved at the multiple stages of the process, including transcription, pre-mRNA processing and translation. UPF1 is one of these enzymes and is conserved in all eukaryotes. Until recently it was understood that UPF1 primarily operates during translation and nonsense mediated mRNA decay (NMD) in the cytoplasm (1), however we recently reported that UPF1 is constantly shuttling between nucleus and cytoplasm. Crucially, our observations show that UPF1 associates with nascent pre-mRNA transcripts and that it plays genome-wide roles in nuclear RNA-based processes – including Pol II transcription and mRNA export - in evolutionary divergent organisms (2-3). These observations change our understanding of the roles of UPF1 in gene expression. They also change current ideas of how this protein might prevent/modifies neurodegenerative diseases such as amyloid lateral sclerosis (ALS). Specifically, we have discovered that depletion of UPF1 leads to nuclear accumulation of RNA aggregates, one of the hallmarks of neurodegeneration. With this project we aim to understand the molecular mechanism of this RNA aggregation in Drosophila models of ALS as well as understanding the import role/s of UPF1 in eukaryotic cells.

References

1. Brogna, S., McLeod, T. and Petric, M. (2016). The Meaning of NMD: Translate or Perish. Trends in Genetics, 32(7), pp.395-407.
2. Singh, A., Choudhury, S., De, S., Zhang, J., Kissane, S., Dwivedi, V., Ramanathan, P., Petric, M., Orsini, L., Hebenstreit, D. and Brogna, S. (2019). The RNA helicase UPF1 associates with mRNAs co-transcriptionally and is required for the release of mRNAs from gene loci. eLife, 8, e41444.
3. De, S et al. Genome-wide chromosomal association of Upf1 is linked to Pol II transcription in Schizosaccharomyces pombe, Nucleic Acids Research, Volume 50, Issue 1, 11 350–367.

Techniques

In addition to training in bioinformatics detailed above, the project will provide advanced training in molecular biology, yeast (or Drosophila) molecular genetics, genomics. The project will involve one or more of the following leading-edge techniques: CRISPR-Cas9 gene editing, NET-seq, ChIP-seq and advanced cell imaging.