Novel functions of UPF1 in safeguarding DNA replication fidelity in S-phase and beyond

Maintaining DNA replication fidelity is required to allow for the successful duplication
of genetic information that will be passed on to the next generation of daughter cells.
Interfering with this process leads to replication stress that can promote mutagenesis,
double-stranded DNA breaks and loss of genetic stability. The fundamental process
of transcription is a well described promotor of DNA replication stress through changes
in chromatin dynamics, DNA structure and direct transcription-replication collisions
(TRCs). In this thesis, we have identified a novel function for the RNA/DNA helicase
UPF1 in preventing harmful consequences between the DNA replicative and
transcriptional machineries. Loss of UPF1 resulted in an increase in spontaneous
transcription-dependent replication fork stalling, double stranded breaks and an
accumulation of R-loops. UPF1-deficient cells following mild replicative stress show a
reduced frequency of replication fork stalling, mitotic delay and the DNA replication
salvage pathway of mitotic DNA synthesis (MiDAS). However, no increase in markers
of under-replicated DNA such as 53BP1 nuclear bodies in the subsequent G1 is
observed, suggesting that cells deficient for UPF1 are able to fully replicate their DNA
prior to mitotic entry under such conditions. Together these data demonstrate UPF1
as vital for protecting the genome from spontaneous TRCs, most likely through its
role in regulating the dissociation of nascent R-loop associated-mRNAs. Loss or
down-regulation of UPF1 also represents a potential mechanism whereby cells could
display resistance to DNA replication-targeting chemotherapeutics. Targeting UPF1-
deficient cancers or UPF1 inhibition with drugs known to synergize with high levels of
TRCs such as PARP inhibitors, could be a promising therapeutic approach.