Zygotic Genome Activation Triggers the DNA Replication Checkpoint at the Midblastula Transition

A conserved feature of the midblastula transition (MBT) is a requirement for a functional DNA replication checkpoint to coordinate cell-cycle remodeling and zygotic genome activation (ZGA). We have investigated what triggers this checkpoint during Drosophila embryogenesis. We find that the magnitude of the checkpoint scales with the quantity of transcriptionally engaged DNA. Measuring RNA polymerase II (Pol II) binding at 20 min intervals over the course of ZGA reveals that the checkpoint coincides with widespread de novo recruitment of Pol II that precedes and does not require a functional checkpoint. This recruitment drives slowing or stalling of DNA replication at transcriptionally engaged loci. Reducing Pol II recruitment in zelda mutants both reduces replication stalling and bypasses the requirement for a functional checkpoint. This suggests a model where the checkpoint functions as a feedback mechanism to remodel the cell cycle in response to nascent ZGA. [Display omitted] •Dosage of transcribed DNA correlates with degree of replication checkpoint activity•Time-resolved RNA Pol II ChIP-seq over the course of zygotic genome activation•Sites of stalled DNA replication overlap with transcribed genomic loci•Reducing zygotic transcription eliminates a genetic requirement for the checkpoint The maternal-to-zygotic transition during early development results in a conflict between de novo RNA polymerase recruitment and ongoing DNA replication. The replication checkpoint functions in this context as a feedback mechanism to drive the initial steps of cell-cycle remodeling in response to increased cellular transcription.