Faithful DNA replication is essential and the induction of replication stress may have profound effects on genomic integrity. This is demonstrated by the formation of DNA double strand breaks (DSBs), considered to be the most toxic DNA lesions, at stalled replication forks. Homologous recombination (HR) has been shown to be involved in the replication stress response and has been suggested for stabilisation, restart and repair of stalled replication forks. However, the HR mechanisms induced by replication stress are still, to a major part, unknown. The present thesis focuses on investigating replication patterns following the induction of replication stress. Further, the consequences of stressed replication are studied by detection of DSB formation and characterisation of HR in mammalian cells.

Here, we have identified WEE1, a regulator of mitotic entry, as a factor required to maintain correct replication. Depletion of WEE1 results in the formation of DSBs specifically in newly replicated DNA, as visualised in a modified pulse field electrophoresis assay. We were also able to detect formation of replication-associated secondary DSBs following treatment with ionizing radiation (IR). These DSBs were further demonstrated as major substrates for IR induced HR.

Using the DNA fibre technique we investigated the effect of DNA alkylating agents on replication. We found that DNA methylations pose direct physical blocks to progressing replication forks causing them to stall in a checkpoint independent manner. Furthermore, we studied restart kinetics following methylation blocked replication and identified a distinct restart mechanism for blocked replication forks independent of new origin firing and HR.

In conclusion, our findings increase the knowledge of replication dynamics following perturbed replication and further clarify the role of HR following IR induced damage and DNA alkylation.