Cell cycle-resolved Hi-C reveals unexpected plasticity of A/B compartments across interphase

The spatial organization of chromatin into active (A) and inactive (B) nuclear compartments is essential for genome regulation, yet their cell-cycle dynamics are poorly understood. Most studies have primarily focused on the events surrounding mitosis and have yielded only limited insight into S-phase chromatin dynamics. To address this gap, we developed a simple, drug-free approach that combines the Fucci cell-cycle indicator with in situ Hi-C to comprehensively analyze A/B compartment dynamics throughout interphase. Unexpectedly, and contrary to prevailing views, we found that A/B compartment strength abruptly increases upon S-phase entry, stabilizes, and subsequently declines in late S/G2. We demonstrate that this abrupt strengthening, a process stably maintained during differentiation that we term 'compartment maturation', requires passage through the G1/S transition but is independent of active DNA synthesis. This maturation involves substantial architectural remodeling, particularly within the A compartment, which consolidates into a more organized structure as individual A domains rearrange to form long-range interactions. Based on these observations, we put forward a revised, stepwise model of nuclear compartmentalization during cell-cycle progression, consisting of four distinct stages: chromosome unfolding (G1), chromatin maturation (G1/S), stabilization (S phase), and refolding (G2). These findings reveal the unexpected plasticity of A/B compartments, underscoring the G1/S transition as a critical period for their reorganization.