Embryonic Stem Cells Maintain High Origin Activity and Slow Forks to Coordinate Replication with Cell Cycle Progression

Embryonic stem (ES) cells are pluripotent stem cells that can produce all cell types of an organism. ES cells proliferate rapidly and are thought to experience high levels of intrinsic replication stress. Here, by investigating replication fork dynamics in substages of S phase, we show that pluripotent stem cells maintain a slow fork speed and high active origin density throughout S phase, with little sign of fork-pausing. In contrast, the fork speed of non-pluripotent cells is slow at the beginning of S phase, accompanied by increased fork-pausing, but thereafter fork-pausing rates decline and fork speed rates accelerate in an ATR-dependent manner. Thus, replication fork dynamics within S phase are distinct between ES and non-ES cells. Nucleoside addition can accelerate fork speed and reduce origin density. However, this causes miscoordination between the completion of DNA replication and cell cycle progression, leading to genome instability. Our study indicates that fork-slowing in the pluripotent stem cells is an integral aspect of DNA replication.