Difference Between Nucleus and Nucleoid

Main Difference – Nucleus vs Nucleoid

Nucleus and nucleoid are the areas which separate the genetic material from other cellular components of the cell. Nucleus is the membrane-enclosed area which houses the eukaryotic genetic material. It consists of organized DNA/protein molecules inside chromatin fibers. Nucleoid is the area which holds prokaryotes’ genetic material in the cytoplasm. It consists of a single chromosome. Both nucleus and nucleoid help to regulate the gene expression. The key difference between nucleus and nucleoid is that nucleus is a membrane-bound organelle in the eukaryotes’ cytoplasm and nucleoid is a particular area in the prokaryotes’ cytoplasm.

This article looks at, 

1. What is a Nucleus
     – Structure, Composition
2. What is a Nucleoid
     – Structure, Composition
3. What is the difference between Nucleus and Nucleoid

Difference Between Nucleus and Nucleoid - Comparison Summary

What is a Nucleus

The nucleus is a membrane-bound organelle which houses the eukaryotes’ genetic material. Most eukaryotic cells contain a single nucleus. The integrity of genes is maintained by the nucleus. It also controls the gene expression. DNA replication, transcription and ribosome biogenesis occur in the nucleus.

Structure and Composition of Nucleus

The nucleus is composed of nuclear envelope which is a double-membrane structure. The aqueous channels within the nuclear membrane are the nuclear pores. Nucleoplasm is the viscous liquid enclosed by the nuclear envelope. The network within the nucleus is called nuclear matrix or the nuclear lamina. It provides mechanical support to the nucleus. Chromosomes are also present in the nucleus. Chromosomes exist as DNA-protein complex called as chromatin. Two types of chromatin can be identified within the nucleus: euchromatin and heterochromatin. Euchromatin is the lesser packed chromatin type which consists of frequently expressed genes. Heterochromatin is the other type of chromatin; this is a more compact form consisting of infrequently transcribing genes. The nucleolus is also a component of the nucleus. The nucleus is a highly organized structure compared to the nucleoid in prokaryotes. Eukaryotes’ nucleus and the prokaryotes’ nucleoid is shown in figure 2.

Difference Between Nucleus and Nucleoid

Figure 1: Nucleus and the nucleoid

What is Nucleoid

Nucleoid is an area in the cytoplasm which houses the prokaryotes’ genetic material. It is an irregular-shaped region. Nucleoid is also called the genophore. The nucleoid is not surrounded by nuclear membranes, unlike eukaryotic nucleus. A single, circular chromosome can be found in the nucleoid of prokaryotes. This chromosome consists of a double-stranded DNA piece. The length of the DNA molecule can be at least a few million base pairs. In addition to this chromosome, some of the genes can be found as circular plasmids inside the cytoplasm of prokaryotes. 

Structure of Nucleoid

The nucleoid can be observed clearly apart from the cytosol under the electron microscope. By staining the DNA with Feulgen stain, the nucleoid can be visualized under the light microscope. In the fluorescent microscopy, ethidiun bromie is widely used to stain nucleoids. The nucleoid in a cell is shown in figure 1. The structure of the nucleoid of some bacteria may change due to exposure to UV. E. coli nucleoid becomes compact with the exposure to UV and this compaction leads to the activation of RecA, which is a DNA damage repair protein.  

Main Difference - Nucleus vs Nucleoid

Figure 1: Nucleoid


Composition of Nucleoid

The nucleoid is composed of 60% DNA. In addition to DNA, it is composed of RNA and proteins. Most of the RNAs are messenger RNA and most of the proteins are transcription factor proteins. These RNA and proteins regulate the gene expression in prokaryotes. These proteins can also associate with DNA to form nucleoid proteins or nucleiod-associated proteins (NAPs). Examples of NAPs are HU, DPS, Fis, H-NS and CbpA. They help the DNA aggregation, bridging, and bending. H-NS, Fis and HU like NAPs form clusters which help to compact specific genomic regions locally or scattered throughout the chromosome. These NAPs also help to coordinate the events of transcription, sequestrate specific genes spatially and regulate the sequestrated genes. On the other hand, histones promote DNA looping. In prokaryotes, histones do not form nucleosomes in the nucleoid.

Difference Between Nucleus and Nucleoid


Nucleus: Nucleus is a membrane-bound organelle in the eukaryotes’ cytoplasm.

Nucleoid: Nucleoid is a particular area in the prokaryotes’ cytoplasm.


Nucleus: This is a large, well-organized structure.

Nucleoid: This is a small, poorly organized structure.

Number of Chromosomes

Nucleus: It contains more than one chromosome.

Nucleoid: A single chromosome exists in the nucleoid.

Chromosome Structure

Nucleus: DNA forms structure with histones which is called chromatin.

Nucleoid: DNA is compact with NAPs.


Nucleus: Nucleolus and nucleoplasm are present.

Nucleoid: Nucleolus and nucleoplasm are absent.


Nucleus: DNA, RNA, enzymes, histones, dissolved ions, and other sub-nuclear bodies can be found in the nucleus.

Nucleoid: DNA, RNA, histones and other proteins for the compaction are found in the nucleoid.


Nucleus: It is a spherical shaped organelle.

Nucleoid: Nucleoid is irregular in shape.


Nucleus: It houses the genetic material and provides the space for transcription, DNA replication, and ribosome biogenesis.

Nucleoid: It only houses the genetic material.


Nucleus and nucleoid house the genetic material of eukaryotes and prokaryotes, respectively. The nucleus is a highly organized structure compared to nucleoid. Nucleus is composed of nucleoplasm and nuclear lamina. Nucleus also contains enzymes required for transcription, DNA replication, and ribosome biogenesis. Ultimately, the nucleus provides space for enzymatic reactions to occur. But, nucleoid is a region in the prokaryotic cytoplasm which only houses DNA. This is the main difference between nucleus and nucleoid.

1. “Nucleoid”. Wikipedia, the free encyclopedia, 2016. Accessed 28 Feb 2017
2. “Cell nucleus”. Wikipedia, the free encyclopedia, 2017. Accessed 28 Feb 2017

Image Courtesy:
1. “Cell types” By Science Primer (National Center for Biotechnology Information). Vectorized by Mortadelo2005. – SVG version of Image:Celltypes.png. (Public Domain) via Commons Wikimedia
2. “OSC Microbio 03 03 Nucleoid” By CNX OpenStax – (CC BY 4.0) via Commons Wikimedia

About the Author: Lakna

Lakna, a graduate in Molecular Biology & Biochemistry, is a Molecular Biologist and has a broad and keen interest in the discovery of nature related things

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