Recurrence plot reconstruction reveals chromosomal reorganization before territory formation

Chromatin conformation capture methods such as Hi-C have improved understanding of nuclear architecture. However, reconstruction from single-cell Hi-C (scHi-C) data is challenging due to limited DNA contacts per cell. We have previously developed the recurrence plot-based reconstruction (RPR) method for reconstructing three-dimensional (3D) genomic structure from Hi-C data even from low-coverage DNA contact information. Here we used the RPR method to analyze scHi-C data derived from early-stage F₁ hybrid embryos as a proof-of-concept for understanding of global chromosomal architecture. We found that paternal and maternal chromosomes become gradually intermingled from the 1-cell to the 64-cell stage, and that discrete chromosome territories are largely established between 8-cell and 64-cell stages. We also observed Rabl-like polarization of chromosomes from the 2- to 8-cell stage, which was mostly dissolved by the 64-cell stage. We also noted transient rod-like extension and parallel chromosome alignment at the 4-cell stage. These findings indicate dynamic chromosomal reorganization before territory formation. RPR and scHi-C together capture 3D chromosomal architecture of individual cells during early embryogenesis.