Chromatin assembly at replication forks enables differentiation of human iPSCs

DNA replication is both productive and disruptive, synthesising new DNA while dismantling chromatin to allow fork progression. Because of its disruptive nature, DNA replication has been suggested to enable chromatin changes facilitating cell fate transitions. However, the role of DNA replication in cell fate transitions remains incompletely understood. Here we show that upon differentiation of human induced Pluripotent Stem Cells (iPSCs) into presomitic mesoderm, DNA replication allows hundreds of proteins, including transcription factors, histone chaperones, and histone methyltransferases, to access chromatin. Moreover, H3K9 methylation is enhanced upon differentiation through a DNA replication-coupled process. Most of the proteins recruited to (or evicted from) nascent chromatin during differentiation are already present in iPSCs, suggesting they may play a role in the early response to differentiation. Among these, we identified ERH and SETDB1 as essential for mesoderm differentiation. Our work reveals a new paradigm to explore: how differentiation signals exploit the replisome interactome to enable rapid chromatin changes.