Schematic of the working model describing how BrdU peaks represent hotspot sites of replication forks slow down/pausing. Panel on the left: if DNA replication progresses unperturbedly through a genomic region in a cell, by averaging the BrdU-Seq signal over a population of cells, we will obtain a relatively flat profile. However, if in a specific site there is a hotspot where replication forks slow down/pause/stall, and this hotspot occurs frequently in a population of cells, when we average the BrdU-Seq signal over that region, the profile will show a peak as there is an overrepresentation of specific reads. We can computationally identify these sites performing a peak calling analysis.
