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Related Experiment Video

Updated: Sep 4, 2025

A Human Bone Marrow 3D Model to Investigate the Dynamics and Interactions Between Resident Cells in Physiological or Tumoral Contexts

A Human Bone Marrow 3D Model to Investigate the Dynamics and Interactions Between Resident Cells in Physiological or Tumoral Contexts

Published on: December 16, 2022

Tough Tissue Hi-C.

¹Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland. sgrob@botinst.uzh.ch.

Methods in Molecular Biology (Clifton, N.J.)

|July 22, 2022

Summary

This study presents an optimized Hi-C protocol for analyzing three-dimensional genome folding, particularly in challenging plant tissues. The improved method ensures high-quality data for genome assembly and evolutionary studies.

Area of Science:

Molecular Biology
Genomics
Evolutionary Biology

Background:

Three-dimensional chromosome folding is crucial for understanding cellular processes and genome assembly.
High-throughput chromosome conformation capture (Hi-C) is the primary method for studying genome architecture.
Existing Hi-C protocols face challenges with difficult-to-process tissues, especially in plants.

Purpose of the Study:

To develop and optimize a Hi-C protocol for efficient genome-wide 3D structure analysis.
To overcome limitations associated with isolating nuclei from tough plant tissues for Hi-C.
To enable de novo genome assembly and evolutionary studies in diverse species.

Main Methods:

Optimization of nuclei isolation from challenging plant and animal tissues.

Keywords:

3D chromosome folding Genome assembly Hi-C Nonmodel species Tough tissues

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Adaptation of the Hi-C protocol for improved sample quality.

Validation of the protocol across various tissue types.

Main Results:

Successful generation of high-quality Hi-C libraries from diverse plant and animal tissues.
Demonstrated effectiveness of the optimized protocol in overcoming tissue-specific challenges.
Facilitation of accurate three-dimensional genome folding analysis.

Conclusions:

The optimized Hi-C protocol significantly enhances the feasibility of studying genome 3D structure.
This method supports genome assembly and evolutionary research in nonmodel organisms.
The protocol provides a robust tool for molecular biologists, evolutionary biologists, and ecologists.