Analysis of chromosomal rearrangements after replication restart

Impediments to DNA replication are known to induce gross chromosomal rearrangements (GCRs) and copy-number variations (CNVs). GCRs and CNVs underlie human genomic disorders and are a feature of cancer. During cancer development, environmental factors and oncogene-driven proliferation promote replication stress. Resulting GCRs and CNVs are proposed to contribute to cancer development and therapy resistance. Using an inducible system that arrests replication forks at a specific locus in fission yeast, chromosomal rearrangement was investigated. In this system, replication restart requires homologous recombination. However, it occurs at the expense of gross chromosomal rearrangements that occur by either faulty template usage at restart or after the correctly restarted fork U-turns at inverted repeats. Both these mechanisms of chromosomal rearrangement generate acentric and reciprocal dicentric chromosomes. The work in this thesis analyses the timing of replication restart and appearance of chromosomal rearrangements in a single cell cycle after induction of fork stalling. This research also identifies the recombination-dependent intermediates corresponding to the two pathways of rearrangements. Moreover, the DNA integrity checkpoint responses after replication fork arrest, homologous recombination dependent replication restart, and the accumulation of GCRs are investigated.