Transcription Restart Establishes Chromatin Accessibility after DNA Replication

DNA replication is highly disruptive to chromatin, leading to eviction of nucleosomes, RNA polymerase and regulatory factors. When and how transcription resumes on DNA following DNA replication is unknown. Here we develop a replication-coupled Assay for Transposase-Accessible Chromatin, repli-ATAC-seq, to investigate active chromatin restoration post-replication in mouse embryonic stem cells. We find nascent chromatin is inaccessible and transcriptionally silent, with accessibility and RNA polymerase occupancy re-appearing within 30 minutes. Chromatin accessibility restores differentially genome-wide, with super enhancers regaining transcription factor occupancy faster than other genomic features. We also identify opportunistic and transient accessible chromatin within gene bodies after replication. Systematic inhibition of transcription shows that transcription restart is required to re-establish active chromatin states genome-wide and resolve opportunistic binding events resulting from DNA replication. Collectively, this establishes a central role for transcription in overcoming the genome-wide chromatin inaccessibility imposed by DNA replication every cell division. Overall design: repli-ATAC-seq time series, RNA polymerase ChOR-seq time series, and repli-ATAC-seq with transcription inhibition in mouse embryonic stem cells.