Integrative analysis and simulations of DNA double-strand break formation reveal cells' heterogeneity in response to replication stress

DNA double-strand breaks (DSBs), the most deleterious form of DNA damage, often arise from slowing replication forks (replication stress). Sequencing allows to detect DSBs genome-wide, but not their population distribution. To infer population distribution of DSBs, we use computer simulations to integrate replication profiling, qDSB-Seq and gel electrophoresis data. By simulating genomic and population distributions of DSBs, we find that forks (~20%) break randomly during replication stress and in major population ~95% of them are repaired and continue replication, while in minor population (~5%) broken forks fail to be repaired causing replication arrested and massive chromosome breakage. We also use computer simulations to clarify mechanisms of action of Mus81 endonuclease. We show that, in the absence of Mec1, Mus81 cleaves 61% of stalled forks. We conclude that computer simulations are powerful tools to analyze and infer genomic and population distribution of DSBs and mechanisms of DSB creation.