Mapping In vivo Nascent Chromatin using EdU and sequencing (MINCE-seq).

Passage of the replication fork disrupts every nucleosome in the genome. It had been believed that nucleosomes reassemble in the same position following replication fork passage. However, the chromatin landscape after fork passage was never mapped. To map the newly replicated chromatin landscape, we developed Mapping In vivo Nascent Chromatin with EdU and sequencing (MINCE-seq).

MINCE-seq can generate a high-resolution map of newly replicated and maturing chromatin without the need for cell sorting or synchronization. Using MINCE-seq, we discovered that nucleosomes replace transcription factors (TFs) at active promoters and enhancers genome-wide after the passage of the replication fork in Drosophila cells. The characteristic nucleosome landscape emerges from a uniformly packaged genome post-replication by the action of TFs, RNA-Polymerase II, and chromatin remodelers after replication fork passage. This study showed that the distinctive chromatin landscapes that reflect cellular identity are erased genome-wide during replication and need to be reestablished post-replication every cell cycle.