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Updated: Apr 20, 2026

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

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

Published on: May 6, 2010

The Hitchhiker's guide to Hi-C analysis: practical guidelines.

Bryan R Lajoie¹, Job Dekker¹, Noam Kaplan¹

¹Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605-0103, USA.

Methods (San Diego, Calif.)

|December 3, 2014

Summary

New genomic tools like chromosome conformation capture (3C) and deep sequencing allow detailed study of chromosome 3D organization. This paper offers guidance for analyzing Hi-C and 3C-seq data on chromatin interactions.

Keywords:

Bioinformatics Chromatin structure Chromosome conformation capture Deep sequencing Hi-C

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Last Updated: Apr 20, 2026

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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Advanced molecular genomic techniques, including chromosome conformation capture (3C) and high-resolution imaging, have revolutionized the study of chromosome spatial organization.
These methods enable genome-wide analysis of how DNA is folded within the nucleus.

Purpose of the Study:

To provide comprehensive guidelines for the analysis and interpretation of data generated by genome-wide 3C-based methods.
To address the specific challenges associated with analyzing deep sequencing data from techniques like Hi-C and 3C-seq.

Main Methods:

Utilizes chromosome conformation capture (3C) methodologies.
Employs deep sequencing for high-throughput data acquisition.
Focuses on analyzing pairwise chromatin interaction data.

Main Results:

Establishes a framework for interpreting complex genomic interaction data.
Highlights best practices for data processing and quality control.
Aims to improve the accuracy and reliability of chromatin interaction mapping.

Conclusions:

Accurate analysis of genome-wide 3C data is crucial for understanding chromosome architecture.
Standardized guidelines will enhance the reproducibility and comparability of chromatin interaction studies.
This work supports researchers in leveraging powerful genomic tools for nuclear organization research.