Transcription–replication conflicts underlie sensitivity to PARP inhibitors

To examine replication fork progression firing upon TIMELESS/TIPIN knockdown, EdUseq was performed in HeLa cells transfected with siCTRL, siTIMELESS or siTIPIN, synchronised with Thymidine and then released for 120 min in S phase, with the last 30 minutes being labeled with EdU. Overall design: Cells were collected by mitotic shake-off and allowed to progress through the cell cycle for 12 hours in the presence of 5-ethynyl2'-deoxyuridine (EdU) and hydroxyurea (HU). EdU-labelled DNA was then isolated and subjected to high-throughput sequencing (EdUseq-HU)