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Related Experiment Video

Updated: Jul 7, 2026

Capturing Chromosome Conformation Across Length Scales

Capturing Chromosome Conformation Across Length Scales

Published on: January 20, 2023

High-resolution circular chromosome conformation capture assay.

Anita Göndör¹, Carole Rougier, Rolf Ohlsson

¹Department of Development and Genetics, Uppsala University, Norbyvägen 18A, S-752 36 Uppsala, Sweden. anita.gondor@ebc.uu.se

Nature Protocols

|February 16, 2008

Summary

This summary is machine-generated.

Circular 3C (4C) sequencing identifies unknown DNA interactions for genome-wide studies. This method maps cis-regulatory elements and aids chromatin mark analysis, offering high-resolution insights.

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

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Area of Science:

Genomics
Molecular Biology
Epigenetics

Background:

Chromosome Conformation Capture (3C) studies chromosomal folding but requires known DNA sequences.
3C's limitation hinders genome-wide interaction analysis.
Circular 3C (4C) overcomes this by identifying unknown interacting sequences.

Purpose of the Study:

To describe a protocol for the 4C method.
To generate a high-resolution interaction map.
To enable analysis of cis-regulatory elements and chromatin marks.

Main Methods:

Formaldehyde cross-linking of living cells.
Enzyme digestion, intramolecular ligation, and quantitative PCR (Q-PCR).
Exploiting a circular intermediate with strategically positioned primers.

Main Results:

The 4C method identifies unknown interacting DNA sequences.
A high-resolution interaction map is generated.
The protocol is optimized for enzyme digestion and amplification.

Conclusions:

4C sequencing provides a powerful tool for genome-wide interaction studies.
The method facilitates analysis of cis-regulatory elements.
4C analysis can be compared with Chromatin Immunoprecipitation (ChIP) on chip data.