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Genomic DNA in Prokaryotes

Genomic DNA in Prokaryotes

The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
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Updated: Jul 9, 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

Hi-C/3C-seq Data Analysis for Prokaryotic Genomes with HiC-Pro.

Naomichi Takemata¹

¹Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan. takemata.naomichi.3a@kyoto-u.ac.jp.

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

|September 16, 2024

Summary

This guide details using the HiC-Pro pipeline for analyzing Hi-C/3C-seq data in prokaryotes. It addresses challenges posed by circular bacterial and archaeal genomes for 3D genome studies.

Keywords:

3C-seq Archaea Bacteria Bioinformatics Hi-C

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

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

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Published on: October 5, 2018

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

Area of Science:

Microbiology
Genomics
Biotechnology

Background:

Studying the 3D genome structure of prokaryotes like bacteria and archaea is challenging due to their small cell size and growth conditions.
Traditional microscopic analyses are often difficult for these organisms.
High-throughput chromosome conformation capture techniques (Hi-C and 3C-seq) offer powerful insights into prokaryotic 3D genome organization.

Purpose of the Study:

To provide a practical guide for analyzing Hi-C/3C-seq data from prokaryotes.
To address the specific analytical challenges associated with circular prokaryotic genomes.

Main Methods:

Utilizing the HiC-Pro bioinformatics pipeline.
Adapting HiC-Pro for prokaryotic Hi-C/3C-seq data analysis.
Implementing specific strategies to handle the circularity of bacterial and archaeal genomes.

Main Results:

A practical workflow for prokaryotic Hi-C/3C-seq data processing using HiC-Pro.
Demonstration of how to overcome analytical hurdles related to circular genomes.
Facilitation of 3D genome structure studies in bacteria and archaea.

Conclusions:

The HiC-Pro pipeline can be effectively adapted for prokaryotic 3D genome studies.
This guide simplifies the analysis of Hi-C/3C-seq data for bacteria and archaea.
Enables deeper understanding of prokaryotic genome organization and function.