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bioRxiv · 10.1101/171439

Integrated analysis of DSB patterns reveals precisely DSB formation mechanisms following replication fork collapse

Zhu, Y.·Biernacka, A.·Pardo, B.·Forey, R.·Dojer, N.·Nde, J.·Fongang, B.·Yousefi, R.·Mitra, A.·Li, J.·Skrzypczak, M.·Kudlicki, A.·Pasero, P.·Ginalski, K.·Rowicka, M.
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Abstract

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.

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Zhu, Y., Biernacka, A., Pardo, B., Forey, R., Dojer, N., Nde, J., Fongang, B., Yousefi, R., Mitra, A., Li, J., Skrzypczak, M., Kudlicki, A., Pasero, P., Ginalski, K., Rowicka, M.. 2017-09-14. Integrated analysis of DSB patterns reveals precisely DSB formation mechanisms following replication fork collapse. https://doi.org/10.1101/171439

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