Replication Stress-Induced Chromatin Loops Protect Forks and Maintain Genome Stability
Replication stress threatens genome stability, requiring protective mechanisms for replication forks. However, the role of chromatin folding in these mechanisms is unclear. Using replication-associated Hi-C, we found that replication stress induces chromatin loops around de novo heterochromatin-enriched replication sites. These loops vary by replication timing: early-replicating regions form fewer loops, maintaining open chromatin, while late-replicating regions form compact loops. Replication forks stall at convergent CTCF motifs, repositioning CTCF to anchor loops, which are stabilized by G9a-mediated heterochromatin. Genome-wide mapping of fork degradation sites revealed that loops protect replication forks from degradation, while un-looped forks are vulnerable. In BRCA2-deficient cells, loops shield replication initiation zones, whereas nascent DNA outside loops degrades and accumulates mutations. Our work highlights the role of stress-induced 3D chromatin folding in protecting forks and maintaining genome integrity.