Modelling an optical replication mapping experiment to measure human DNA replication kinetics

Synopsis

DNA replication is nature's method of copying genetic information, a crucial process facilitated by a set of protein machinery at specific sites called ``replication origins.'' The spatiotemporal organization of these origins, known as the ``replication program,'' governs DNA replication timing, a topic of longstanding interest in biology. Various experimental approaches, such as DNA combing and DNA sequencing, have been employed to measure the replication program, particularly in bacterial and simple eukaryotic systems. However, these methods face challenges when applied to human genomes, owing to their longer length and higher stochasticity. Optical Replication Mapping (ORM) has emerged as a novel experimental approach capable of providing single-molecule, genome-wide, and high-throughput data on the replication process. Nonetheless, ORM experiments suffer from sparse labeling, necessitating a model to understand label distribution around origins. In this thesis, we show that a previously used model for label incorporation is incomplete. In response, we have refined the model by introducing further physical assumptions. Despite these refinements, the more elaborate models still fall short of explaining ORM data comprehensively.