PT  - JOURNAL ARTICLE
AU  - Yingjie Zhu
AU  - Anna Biernacka
AU  - Benjamin Pardo
AU  - Romain Forey
AU  - Norbert Dojer
AU  - Raziyeh Yousefi
AU  - Jules Nde
AU  - Bernard Fongang
AU  - Abhishek Mitra
AU  - Ji Li
AU  - Magdalena Skrzypczak
AU  - Andrzej Kudlicki
AU  - Philippe Pasero
AU  - Krzysztof Ginalski
AU  - Maga Rowicka
TI  - Integrated analysis of patterns of DNA breaks reveals break formation mechanisms and their population distribution during replication stress
AID  - 10.1101/171439
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 171439
4099  - http://biorxiv.org/content/early/2017/09/18/171439.short
4100  - http://biorxiv.org/content/early/2017/09/18/171439.full
AB  - DNA double-strand breaks (DSBs) can be detected by label-based sequencing or pulsed-field gel electrophoresis (PFGE). Sequencing yields population-average DSB frequencies genome-wide, while PFGE reveals percentages of broken chromosomes. We constructed a mathematical framework to combine advantages of both: high-resolution DSB locations and their population distribution. We also use sequencing read patterns to identify replication-induced DSBs and active replication origins. We describe changes in spatiotemporal replication program upon hydroxyurea-induced replication stress. We found that one-ended DSBs, resulting from collapsed replication forks, are population-representative, while majority of two-ended DSBs (79-100%) are not. To study replication fork collapse, we used strains lacking the checkpoint protein Mec1 and the endonuclease Mus81 and quantified that 19% and 13% of hydroxyurea-induced one-ended DSBs are Mec1-and Mus81-dependent, respectively. We also clarified that Mus81-induced one-ended DSBs are Mec1-dependent.