[SS17] Organization of intracellular structures

[SS17-01] Chromatin replication probed by molecular dynamics simulations and nanopore sequencing

*Tsuyoshi Terakawa¹ (1. Department of Biophysics, Kyoto University (Japan))

Keywords:

Chromatin replication,Histone recycling,Molecular dynamics simulation,In vitro reconstitution,Nanopore sequencing

Histone recycling secures epigenetic inheritance by transferring parental histones onto daughter DNA strands. Balanced recycling between leading and lagging strands maintains cellular identity, whereas asymmetry fosters differentiation. Using coarse-grained molecular dynamics simulations, we found that histones are recycled through Cdc45-mediated and unmediated pathways. Cdc45’s acidic loop strengthens electrostatic histone interactions, boosting leading-strand recycling. RPA binding to lagging-strand ssDNA reduces Cdc45-unmediated recycling, while Polε guides histone allocation. Our combined in vitro chromatin replication reconstitution, nanopore sequencing, and deep learning approach called “Repli-pore-seq” revealed symmetrical histone recycling even without Fen1/Cdc9. Histone placement depends on DNA sequence, with GC-rich regions showing strand discordance. Removing Polδ disrupts symmetry, whereas deleting Ctf4 or Csm3/Tof1 shifts histone locations. This framework advances our understanding of DNA replication-coupled histone recycling.