Quantitative in vivo measurement of fork velocity by deep sequencing

DNA is the substrate for many competing biological processes in vivo. Recent experiments have revealed that transcription is subject to conflicts which stall the replication fork and predict that the replication fork velocity may vary significantly over the genome. Here, we demonstrate a novel approach to measuring the locus-dependent in vivo replication fork velocity by deep sequencing and test a number of mechanisms for replication slowdown, including transcription-replication conflicts. We expect this approach to be widely applicable to other biological systems.