Automated mapping of DNA replication fork progression in human cells with ForkML
- Victoria Rojat
- Diletta Ciardo
- Alan Tourancheau
- Florence Proux
- Etienne Jean
- Jean-Michel Arbona
- Benjamin Audit
- Gael A. Millot
- Frédéric Bonhomme
- Paola B. Arimondo
- Olivier Hyrien
- Benoît Le Tallec
2026-01-23
Current approaches to mapping fork progression in the human genome suffer from drastically low throughput. Here, we introduce ForkML, a nanopore sequencing-based method automatically positioning thousands of individual fork velocities by tracking BrdU incorporation into replicating DNA after double pulse-labelling of asynchronous cells. ForkML recovers known human fork speed, accurately detects replication stress, and, crucially, connects replication dynamics to genomic and chromatin contexts, exposing fork slowdown in early-replicating transcribed regions.