Recurrence plot reconstruction reveals chromosomal reorganization before territory formation

Area of Science:

• Genomics
• Developmental Biology
• Cell Biology

Background:

• Chromatin conformation capture (Hi-C) methods advance nuclear architecture understanding.
• Reconstructing 3D genome structure from low-contact single-cell Hi-C (scHi-C) data is challenging.

Purpose of the Study:

• To apply the recurrence plot-based reconstruction (RPR) method to scHi-C data for analyzing early embryonic 3D genome organization.
• To investigate dynamic chromosomal reorganization and territory formation during early embryogenesis.

Main Methods:

• Utilized the recurrence plot-based reconstruction (RPR) method.
• Analyzed single-cell Hi-C (scHi-C) data from early-stage F1 hybrid embryos.

Main Results:

• Paternal and maternal chromosomes gradually intermingled from 1-cell to 64-cell stages.
• Discrete chromosome territories were established between the 8-cell and 64-cell stages.
• Observed Rabl-like polarization, transient rod-like extension, and parallel chromosome alignment, indicating dynamic reorganization before territory formation.

Conclusions:

• The RPR method effectively reconstructs 3D genome architecture from scHi-C data.
• scHi-C combined with RPR captures dynamic 3D chromosomal architecture during early embryogenesis.
• Early embryogenesis involves significant chromosomal reorganization prior to the establishment of distinct territories.