Replication fork movement sets chromatin loop size and origin choice in mammalian cells

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Abstract
In mammalian cells, the genome undergoes one round of replication per cell cycle. Many origins of replication are never fired, but they serve as a reservoir to be activated if part of the genome is in danger of not being replicated — when progression of a replication fork stalls, for example. Courbet et al. show that latent origins can also be activated by slowing of replication fork progression, and this influences the size of the chromatin loop. In addition, they find that origins located nearby the attachment point of chromatin loops to the nuclear matrix are preferentially activated in the next cell cycle. Genome stability requires one, and only one, DNA duplication at each S phase. The mechanisms preventing origin firing on newly replicated DNA are well documented1, but much less is known about the mechanisms controlling the spacing of initiation events2,3, namely the completion of DNA replication. Here we show that origin use in Chinese hamster cells depends on both the movement of the replication forks and the organization of chromatin loops. We found that slowing the replication speed triggers the recruitment of latent origins within minutes, allowing the completion of S phase in a timely fashion. When slowly replicating cells are shifted to conditions of fast fork progression, although the decrease in the overall number of active origins occurs within 2 h, the cells still have to go through a complete cell cycle before the efficiency specific to each origin is restored. We observed a strict correlation between replication speed during a given S phase and the size of chromatin loops in the next G1 phase. Furthermore, we found that origins located at or near sites of anchorage of chromatin loops in G1 are activated preferentially in the following S phase. These data suggest a mechanism of origin programming in which replication speed determines the spacing of anchorage regions of chromatin loops, that, in turn, controls the choice of initiation sites.