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Related Experiment Video

Updated: Jul 27, 2025

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

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

Published on: October 14, 2022

scGHOST: Identifying single-cell 3D genome subcompartments.

Kyle Xiong¹, Ruochi Zhang¹, Jian Ma¹

¹Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

Biorxiv : the Preprint Server for Biology

|June 9, 2023

Summary

This summary is machine-generated.

New computational method scGhost enables annotation of single-cell 3D genome subcompartments using single-cell Hi-C data. This advances understanding of genome organization variability and its link to gene expression across individual cells.

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Last Updated: Jul 27, 2025

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

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Published on: October 14, 2022

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

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Published on: May 6, 2010

3D Multicolor DNA FISH Tool to Study Nuclear Architecture in Human Primary Cells

3D Multicolor DNA FISH Tool to Study Nuclear Architecture in Human Primary Cells

Published on: January 25, 2020

Area of Science:

Genomics
Computational Biology
Cell Biology

Background:

Single-cell Hi-C (scHi-C) technologies allow investigation of 3D genome organization variability at the single-cell level.
Existing computational methods analyze features like A/B compartments and chromatin loops but lack single-cell subcompartment annotation.
Subcompartments offer a refined view of large-scale chromosome spatial organization crucial for understanding cellular function.

Approach:

Introduced scGhost, a novel computational method for single-cell subcompartment annotation.
scGhost utilizes graph embedding and constrained random walk sampling for robust analysis.
Validated scGhost on both scHi-C and 3D genome imaging data.

Key Points:

scGhost reliably identifies single-cell subcompartments, revealing cell-to-cell variability in nuclear organization.
Application to human prefrontal cortex data identified cell type-specific subcompartments.
These subcompartments show strong correlations with cell type-specific gene expression patterns.

Conclusions:

scGhost provides an effective new tool for annotating single-cell 3D genome subcompartments from scHi-C data.
The method offers insights into the functional implications of subcompartment organization at the single-cell level.
scGhost is applicable to diverse biological contexts for studying genome organization.