Elucidation of genomic information of classical DNA replication foci

It is well known that when the fluorescent nucleotides such as Cy3-dCTP are introduced into living mammalian cells and then incorporated into particular replicated regions of the genome, fluorescently labeled chromatin domains called 'DNA replication foci' are formed in the cells. It is assumed that each focus harbors ~1Mb genome region containing several replication units/forks. Although behaviors of the replication foci in living cells have been well studied, their genomic nature is still largely unknown. This time, to determine their genomic sequences, Cy3-dCTP were introduced into the early S-phase human cells and then the early replication foci were formed, which presumably correspond to euchromatin regions. The genomic DNA fragments that constitute the foci were isolated using anti-Cy3 antibody, and sequenced them by NGS. We found that the early DNA replication foci regions mapped on the genome are well consistent with the active chromatin marks and Hi-C domains, providing new insight into chromatin organization and dynamics.