# HIRA defines early replication initiation zones independently of their genome compartment

## TL;DR

This study shows that HIRA, a histone chaperone, influences early DNA replication zones independently of chromatin structure and accessibility.

## Contribution

The paper uncovers that HIRA regulates early replication initiation separately from chromatin accessibility and 3D genome organization.

## Key findings

- HIRA absence reduces H3.3 enrichment in compartment A without altering histone PTMs.
- Early replication initiation at HIRA-dependent IZs is impaired without changes in chromatin accessibility.
- HIRA complementation restores early IZs and H3.3 enrichment without reversing compartment changes.

## Abstract

Chromatin states and 3D architecture have been used as proxy to identify replication initiation zones (IZs) in mammalian cells, yet their functional interconnections remain a puzzle. Here, to dissect these relationships, we focus on the histone H3.3 chaperone HIRA recently implicated in early initiation zone (IZ) definition. We monitor 3D organisation, chromatin accessibility and histone post-translational modifications (PTMs) in wild-type and HIRA knock-out cells in parallel with early replication initiation. In the absence of HIRA, compartment A loses H3.3 enrichment and gains accessibility without changes in associated histone post-translational modifications (PTMs). Furthermore, impaired early firing at HIRA-dependent IZs does not correspond to changes in chromatin accessibility or patterns of histone H3 PTMs. Additionally, a small subset of early IZs initially in compartment A switch to B and lose early initiation in the absence of HIRA. Critically, HIRA complementation restores these early IZ, and H3.3 variant enrichment, without substantial compartment reversal. Thus, while HIRA contributes to compartment A features, its role in regulating early replication initiation can be uncoupled from accessibility, histone marks and compartment organisation.

Karagyozova at al. reveal that the histone H3.3 chaperone HIRA impacts higher-order spatial arrangement of chromatin, independently from its role in regulating early replication, providing a model to disentangle long-standing correlations between early replication, accessibility, typical histone marks and A compartment.