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

Highlights

• Dual deposition of new H3.1 and H3.3 maintains H3.1/H3.3 boundaries during S phase

• H3 boundaries mark early replication zones independently of active transcription

• HIRA-dependent H3.3 deposition preserves H3 boundaries and early replication zones

• HIRA loss erases early replication zones in non-transcribed regions

Summary

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.