Capturing Three-Dimensional Genome Organization in Individual Cells by Single-Cell Hi-C

Area of Science:

• Genomics
• Molecular Biology
• Epigenetics

Background:

• High-throughput chromosome conformation capture (Hi-C) analyzes genome-wide chromatin organization averaged from cell populations.
• Existing Hi-C methods provide population-level insights into higher-order chromatin structures.
• Limitations exist in resolving cell-to-cell variability in genome conformation using ensemble Hi-C.

Purpose of the Study:

• To develop a single-cell Hi-C method for analyzing genome conformations at the individual cell level.
• To investigate cell-to-cell variability in genome folding and topological domain organization.
• To assess the technical noise and data quality of single-cell Hi-C compared to ensemble Hi-C.

Main Methods:

• Developed a single-cell Hi-C protocol where proximity-dependent ligation occurs within the nucleus.
• Enabled the generation of Hi-C libraries and data from individual cells.
• Applied the method to study genome conformations and identify topological domains.

Main Results:

• Demonstrated conserved topological domain organization across individual cells.
• Observed significant cell-to-cell variability in interdomain contacts and genome-wide chromosome folding.
• Single-cell Hi-C yielded cleaner data with reduced technical noise compared to ensemble methods.

Conclusions:

• Single-cell Hi-C is a viable method for dissecting genome conformation heterogeneity.
• The technique provides insights into conserved and variable aspects of chromosome organization.
• Single-cell Hi-C has the potential to improve ensemble Hi-C by reducing technical noise.