The replication checkpoint couples fork progression to the release of transcribed genes from nuclear pores

The nuclear envelope contributes to chromatin compartmentalization in eukaryotes by anchoring heterochromatin to the lamina and active transcription sites to nuclear pore complexes (NPCs). During DNA replication, chromatin association with the nuclear envelope is thought to act as a topological barrier to DNA polymerases, potentially exacerbating transcription-replication conflicts (TRCs). While limited evidence suggests that the DNA replication checkpoint kinase Rad53/CHK1 promotes the release of genes from the NPC during replicative stress, the global scale and precise regulation of this process remain unknown. Through a candidate-based screen, we demonstrate that gene release from NPCs is a general feature of the cellular response to replication stress, tightly coordinated with replication fork progression. We show that the checkpoint kinases Mec1/ATR and Rad53/CHK1 are both essential for managing gene association with NPCs, but operate in a distinct, stepwise manner: Mec1/ATR triggers the initial dissociation by promoting the removal of RNAPII from the DNA, while Rad53/CHK1 prevents the premature reassociation of transcribed loci by phosphorylating the nucleoporin Mlp1. Finally, we demonstrate that maintaining this control over genes-NPC association is critical for efficient DNA replication under stress. Collectively, our findings reveal that the DNA replication checkpoint integrates genome duplication with chromosome spatial positioning to maintain genome integrity during replication stress.