Chromatin contacts within a fountain-like structure

Hundreds of DNA replication forks functioning simultaneously are essential for timely DNA duplication, but the organization of replication forks are poorly understood in mammalian cells. Here, we developed a replication-enriched in situ HiC (Repli-HiC) method to capture chromatin contacts located adjacent to replication forks and found two types of fountain-like chromatin contacts at thousands of loci. Interactions within fountain-spanning regions are confirmed by q3C-seq analysis of different stages of S phase cells. Three primers, two located within a fountain (Proximal and Distal) and one located outside the fountain, are used to clone the chromatin interaction in the G1, S1, S2, S3, S4, S5, and S6 phase cells.