HIRA-dependent boundaries between H3 variants shape early replication in mammals

The lack of a consensus DNA sequence defining replication origins in mammals has led researchers to consider chromatin as a means to specify these regions. However, to date, there is no mechanistic understanding of how this could be achieved and maintained given that nucleosome disruption occurs with each fork passage and with transcription. Here, by genome-wide mapping of the de novo deposition of the histone variants H3.1 and H3.3 in human cells during S phase, we identified how their dual deposition mode ensures a stable marking with H3.3 flanked on both sides by H3.1. These H3.1/H3.3 boundaries correspond to the initiation zones of early origins. Loss of the H3.3 chaperone HIRA leads to the concomitant disruption of H3.1/H3.3 boundaries and initiation zones. We propose that the HIRA-dependent deposition of H3.3 preserves H3.1/H3.3 boundaries by protecting them from H3.1 invasion linked to fork progression, contributing to a chromatin-based definition of early replication zones.

Automated summary

This study reveals the dual deposition mode of histone variants H3.1 and H3.3 in human cells during S phase, which ensures a stable marking with H3.3 flanked on both sides by H3.1. The H3.1/H3.3 boundaries correspond to the initiation zones of early origins, and the HIRA-dependent deposition of H3.3 plays a crucial role in preserving these boundaries and contributing to the chromatin-based definition of early replication zones.