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Updated: Mar 8, 2026

Capturing Chromosome Conformation Across Length Scales

Capturing Chromosome Conformation Across Length Scales

Published on: January 20, 2023

Massively multiplex single-cell Hi-C.

Vijay Ramani¹, Xinxian Deng², Ruolan Qiu¹

¹Department of Genome Sciences, University of Washington, Seattle, Washington, USA.

|January 31, 2017

Summary

This summary is machine-generated.

We developed single-cell combinatorial indexed Hi-C (sciHi-C) to analyze chromosome conformation in thousands of individual cells. This method reveals cell-to-cell differences in genome structure, advancing single-cell genomics.

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Last Updated: Mar 8, 2026

Capturing Chromosome Conformation Across Length Scales

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Published on: January 20, 2023

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

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Published on: October 14, 2022

Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

Published on: April 21, 2023

Area of Science:

Genomics
Molecular Biology
Cell Biology

Background:

Chromosome conformation capture (3C) methods provide insights into 3D genome organization.
Existing methods often lack the resolution to capture cell-to-cell heterogeneity.
Single-cell genomics aims to dissect biological systems at the individual cell level.

Purpose of the Study:

To introduce single-cell combinatorial indexed Hi-C (sciHi-C), a novel method for analyzing genome-wide chromatin interactions in single cells.
To demonstrate the feasibility and utility of sciHi-C in capturing cell-to-cell variability.
To establish combinatorial indexing as a versatile strategy for single-cell genomic applications.

Main Methods:

Adaptation of the Hi-C technique using combinatorial cellular indexing.
Generation and sequencing of six sciHi-C libraries from a total of 10,696 single cells.
Computational analysis of sciHi-C data to resolve individual cellular conformations.

Main Results:

Successful generation of high-throughput single-cell Hi-C data.
Identification of cell-to-cell heterogeneity in mammalian chromosomal conformation.
Distinguishing cells based on karyotypic and cell-cycle states using sciHi-C data.

Conclusions:

Combinatorial indexing is a powerful and generalizable strategy for single-cell genomics.
sciHi-C enables the study of genome architecture heterogeneity at an unprecedented scale.
This method opens new avenues for understanding cell-specific genome functions.