“The euchromatin region is known as the gene-rich region while the heterochromatin region is known as gene less region.” 

The euchromatin and heterochromatin regions are present on chromosomes and are the type of chromatin. The chromosomes are the highest level of condensed form of DNA which is made up of two pairs of sister chromatids.

The chromatids are formed by the network of chromatin fibers. 

A chromosome is an inheritance unit of a cell made up of DNA and proteins. 

To make DNA fit inside the cell nucleus the DNA interacts with the histone proteins and manufactures a chromosome via nucleosome, bead-on-string, chromatin and chromatids. 

The entire process of DNA to chromosome is known as DNA packaging. The process of packaging is so crucial to facilitate replication, transcription and translation. 

The chromosome manufacture during the metaphase stage of the cell division however, the chromatin regions (euchromatin and heterochromatin) are vision only during the interphase. 

And henceforth it is known as interphase chromatins. 

Both types of chromatins viz the euchromatin and heterochromatin are different in terms of structure and function. 

To understand the present topic very precisely, we need to first understand what the chromatin is. For that, you can read our previous article: Inside the chromatin.

Let me explain to you in brief, chromatin is a higher level of DNA and protein organization which makes two distinct regions, one took part in transcription while the other one is transcriptionally inactive. 

The inactive or transcriptionally inactive portion of our genome is known as non-coding DNA or gene fewer regions. It actually does not manufacture proteins but helps in regulating gene expression, indeed. 

In the present article, we will understand how the euchromatin and heterochromatin regions are different, it’s structure and its importance in gene expression. 

Related article: Inside Chromatin: Definition, Structure, and Function.

Differences between Euchromatin vs Heterochromatin: 

The euchromatin structure is a loosely packed, less organized chromatin whilst the heterochromatin region is tightly packed and most condense chromatin structure. 

Structurally, the histone proteins play an important role in deciding which type of chromatin to form during the DNA packaging process. 

Further to this, the euchromatin region is fixed or can’t spread while the heterochromatin region can spread into the euchromatin region. This means that genes may become inactive as per the signal given by a cell. 

But thanks to the histone-modifying enzymes, the boundaries between the euchromatin and heterochromatin regions are defined. Inactivation of genes may cause serious health issues.

The euchromatin region is considered a genetically active region while the heterochromatin region is considered a genetically inactive region. 

Now let us understand the reason why!

The euchromatin is loosely packed which means the histone and DNA interaction are loose, this allows enzymes to bind on DNA and perform metabolic reactions like transcription. 

But it is not a case with the heterochromatin region, here, the DNA is so tightly packed or wrapped with protein and does not allow enzymes to locate on it. 

Consequently, transcription can’t happen. 

The graphical representation of how euchromatin and heterochromatin look during the interphase.

As we know transcription is an intermediate stage in protein formation, it must be performed by a cell. 

Therefore the euchromatin regions are transcriptionally active and make a protein while the heterochromatin regions are transcriptionally inactive and can’t form a protein. 

In terms of replication, the euchromatin region is the collection of early replicative chromatins while the heterochromatin region is a collection of late replicating chromatins. 

Here also, the reason is the same. The heterochromatin is so compact that polymerase can’t do replication as fast as the euchromatin region, henceforth, the euchromatin replicates early while the rest are replication late. 

As I said, protein only formed from the euchromatin portion, it is referred to as ‘gene-rich regions’ while the heterochromatin regions are referred to as ‘gene less region’.

Genes are function pieces of DNA that make protein, Therefore almost all the genes are located in the euchromatin region. But not in the heterochromatin region. 

Their property to transcribe into protein makes the euchromatin region more genetically variable. It can produce variabilities. On the other side, the heterochromatin region is so dense that it maintains the structural integrity of the genome. 

Thus in terms of function, the euchromatin regions form proteins while the heterochromatin regions regulate gene expression and maintain the integrity of the genome. 

Chromosomes are located in the nucleus of a cell but the central portion of the nucleus is rich in euchromatin means transcriptionally active chromatins are present in the inner side of the nucleus while the inactive (heterochromatin) regions are located in the periphery of the nucleus during the interphase of cell division. 

Only around 2% of the genomic portion is genetically active or contains genes while the rest is inactive. 

The euchromatin has low DNA density while heterochromatin has high DNA density. 

The gene-rich region- euchromatin is commonly found in both prokaryotic as well as eukaryotic organisms. But the heterochromatin is not present in prokaryotes. 

The prokaryotic genome is so simple and small, it contains less non-coding regions. The activity of gene expression and protein formation is regulated by the model known as opens. 

The euchromatin present in a single form whilst the heterochromatin region is further divided into two portions viz the constitutive heterochromatin region and the facultative heterochromatin region. 

Active genomic elements like the exons or the exonic sequences are located in the euchromatin region while other non-coding, intervening and regulatory sequences are located in the heterochromatin part. 

So far we have discussed so many differences between the euchromatin and heterochromatin,  But the question arises in mind that how someone discriminates between both the regions, how is it visible? 

A technique known as karyotyping is utilized to see chromosomes. Techniques like the Giemsa-trypsin-Giemsa banding manufacture various banding patterns on the chromosomes, using which we can discriminate different chromosomes. 

Now here the next big thing comes!

The euchromatin region stains lightly while the heterochromatin region stains darker by GTG banding. 

The reason is that the loosely packed DNA of euchromatin absorbs less stain in comparison with the denser heterochromatin region. We have the image of it here: 

The real image of GTG banded chromosomes showing the euchromatin region and heterochromatin region on chromosomes.

The euchromatin is located on the arms of the chromosome while the heterochromatin is located in the centromeric and telomeric portion of the chromosomes, majorly. 

If we discuss the molecular structure of both the nature of nucleotide sequences also vary between both. 

The euchromatin is simple, repetitive less GC rich nucleotide sequences while the heterochromatin is the complex, repetitive, and high GC rich nucleotide sequences. 

Similarities between euchromatin and heterochromatin:

There are so many differences between the two types of chromatins, though, they have some similarities as well. 

Both are the sequences of DNA made up of a chain of nucleotides. Though perform different functions. 

Both are the type of chromatin that is made up of the nucleosome assemblies and play a key role in organizing DNA on chromosomes. 

The euchromatin and heterochromatin are visible more distinctly during the interphase stage of the cell division.

Both chromatins can only interact with a special type of protein known as histones. 

Euchromatin in a nutshell: 

Only around 1.8% to 2.0% region of a human genome is gene-rich segments, meaning, the euchromatin. 

The DNA sequences of the euchromatin region are actively involved in the replication, transcription and translation and thus form proteins. 

The euchromatin regions look light pink under the microscope. 

In the nucleus, the euchromatin region appears in the middle scattered to allow enzymes to perform various catalytic reactions. 

Related article: Differences Between Chromosome and Chromatid.

Heterochromatin in the nutshell: 

The 98% portion of the genome is a transcriptionally inactive- heterochromatin region. It appears darker under the microscope. 

Although it can’t tailor proteins, it regulates the expression of genes. The heterochromatin regions are not present in the prokaryotic genome or are comparatively less. 

In the nucleus, it appears near the nuclear membrane as darkly stained, irregular dense particles. Two types of heterochromatin are present in the genome; constitutive heterochromatin and facultative heterochromatin.

Frankly speaking, both terms are a bit tedious to understand, at least for a beginner because it is more detailed. Let me try to explain it to you. 

The location of constitutive heterochromatin regions is fixed on chromosomes, commonly found in telomere and centromere. Although the facultative one is not fixed. 

Simply put, the constitutive heterochromatin is totally inactive and repetitive sequences while the facultative heterochromatin is variable, in some cells it may convert into euchromatin and turn on transcription. And this one is the main difference between both. 

This is the reason, the constitutive regions are unchanged between cells or organisms while the facultative one is not consistent between cells. 

For example, the region on chromosome, 1, 9, 16, and Y chromosome of males are unexpressed constitutive regions while the inactive one X chromosome is the example of facultative heterochromatin. 

Here one X chromosome in a female becomes inactive to regulate gene expression but not totally or not in all cells. We will understand the process of X chromosome inactivation in some other article. 

Final verdict: 

Though euchromatin and heterochromatin are different, the heterochromatin region can spread and become euchromatin but the reverse is not possible for euchromatin. 

Also, not all the regions of the heterochromatin portion are inactive, as per the recent findings. Some sequences may undergo transcription and make RNA but can’t form a protein. It helps in gene regulation, instead. 

By forming a complex like RISC, RNAi mediated gene regulation is the pivotal process in the eukaryotic genome. 

The genome of us is a mysterious thing! Follows complex pathways and changes rapidly in variable conditions. 

Also, there is another point to discuss here. The heterochromatin regions are not there in prokaryotes which means the repetitive DNA evolved late during the evolution process.
Means, a functional portion is existing in the living entity but not the non-functional one. It evolved late to actually regulate the expression of genes. 


The process of DNA to protein formation is a complex one! Many enzymes, DNA sequences and regulatory elements are involved in it. The transition from the euchromatin region to heterochromatin plays an important role in gene expression. 

Abnormal euchromatin profile or heterochromatin profile may cause several health problems. 

Conclusively, the main difference between the euchromatin and heterochromatin regions is their role in transcription. One is transcriptionally active while another is transcriptionally active.

The overall function of chromatins is to form protein and regulate the expression of genes.