Difference Between Prokaryotic and Eukaryotic Transcription

Main Difference – Prokaryotic vs. Eukaryotic Transcription

Prokaryotic transcription occurs in the cell cytoplasm and, in prokaryotes, both transcription and translation happen simultaneously. Eukaryotic transcription occurs in the cell nucleus and, in eukaryotes, transcription and translation differ in space and time.

Before getting to know the difference between Prokaryotic and Eukaryotic Transcription in detail, let us first look at the process of transcription. Transcription is the process of making an RNA molecule using one of the DNA strands as the template. Here, the information in the DNA is transcribed or copied to a messenger RNA (mRNA) molecule. Then this mRNA is transported to the cytoplasm where it is translated into a functional protein molecule with the help of numerous enzymes.

Transcription requires three major components:

DNA template (template strand) – only one strand of DNA molecule is used for the transcription

The raw materials such as ribonucleoside triphosphate (rNTPs)

The transcription apparatus – the enzymes required to start and ongoing process of transcription

The process of transcription consists of three stages; initiation, elongation, and termination.

Initiation – transcription apparatus assembles on the promoter and starts the synthesis of RNA.

Elongation – RNA polymerase read through the DNA template strand while unwinding the double helix DNA and add new nucleotides, one at a time, to the 3’ end of the synthesizing RNA strand.

Termination – recognition of the end of the transcription unit and the separation of the RNA molecule from the DNA template.

What is Prokaryotic Transcription

Prokaryotes don’t have an organized nucleus, so the nuclear materials or DNA is in the cytoplasm. Therefore, the transcription occurs in the cytoplasm and all the precursors needed for the transcription are found in the cytoplasm. Prokaryotic transcription requires the RNA polymerase enzyme in order for the transcription to be successfully completed. The enzyme contains five subunits (α, β, β’, ω) and it binds to the sigma factor and the promoter region, and then initiate the transcription by completing the holoenzyme. In prokaryotes, DNA is not bound to histones. Thus, the transcription initiates directly. This could be advantageous when prokaryotes have overlapping genes. Transcription starts at the promoter region and elongate through the coding region and ends when the RNA polymerase reads the termination signal. There are two types of termination signals, Rho-dependent and independent. Transcribed mRNA will be completely translated during the transcription, and no post-transcription processing will be undergoing most of the time.

Difference between Prokaryotic and Eukaryotic Transcription

Typical prokaryotic cell

What is Eukaryotic Transcription

Eukaryotic transcription is more complex than eukaryotic transcription and occurs inside the nucleus. Unlike prokaryotes, eukaryotes contain five types of RNA polymerases according to the need of transcription and contain 10 – 17 subunits. For example, RNA polymerase I transcribe large mRNA and RNA polymerase II transcribe snRNA, snoRNA, and miRNA, etc. These five enzymes found differently in organisms, for example, RNA polymerase IV and V are present only in plants.

Type of RNA polymerase

Transcribing molecules

RNA polymerase I

Large rRNA

RNA polymerase II

Pre- mRNA, some snRNAs, snoRNAs, some miRNAs

RNA polymerase III

tRNAs, small rRNAs, some snRNAs, some miRNAs

RNA polymerase IV

Some miRNAs

RNA polymerase V

RNA molecules taking part in heterochromatin formation

First, the DNA detaches from histone proteins and unwinds near the promoter region. RNA polymerase and other transcription factors including enhancers will be bound to the promoter region. Transcription starts at the transcription initiation site and goes up to the transcription termination signal. Unlike prokaryotes, the transcript is very long and goes through extensive processing. Newly formed mRNA is called pre-mRNA. This is processed by slicing out the non-coding region, and coding regions will be joined back together. This is called the mature mRNA, and it is ready to be translated. This is the complete process of transcription.

Main Difference - Prokaryotic vs. Eukaryotic Transcription

Eukaryotic cell (Animal)

Difference Between Prokaryotic and Eukaryotic Transcription


Prokaryotic transcription occurs in the cell cytoplasm.

Eukaryotic transcription occurs in the cell nucleus.

Transcription and Translation

In Prokaryotic transcription, transcription and translation happen simultaneously.

In Eukaryotic transcription, transcription and translation differ in space and time (transcription – nucleus, translation – cytoplasm)

Transcription of mRNA

In Prokaryotic transcription, mRNA is transcribed directly from template DNA molecule.

In Eukaryotic transcription, initially a pre-mRNA molecule (primary transcript) is formed and then processed to yield a mature mRNA.

Type of mRNA

In Prokaryotic transcription, the type of RNA polymerase does not vary with the bacterial type.

In eukaryotes transcription, the type of RNA varies with the organisms.

e.g.  RNA polymerase I, II, III are present in all eukaryotes, but RNA polymerase IV and V are only present in plants

RNA Polymerase

A single type of RNA polymerase, which has a core enzyme and other subunits, is involved in prokaryotic transcription.

Type of RNA polymerase varies according to the type of RNA that is transcribed in the eukaryotic cells. (i.e. They identify different type of promoters)


Prokaryotic RNA polymerase consists of five subunits (α,β,β’,ω)

Eukaryotic RNA polymerase consists of 10 – 17 subunits.

Promoter Recognition

In prokaryotes, holoenzyme (RNA polymerase + sigma factor) recognizes and binds directly to the promoter.

In eukaryotes, promoter recognition cannot be carried out by RNA polymerase alone, but accessory proteins in the cell should recognize the promoter, thereby recruiting a specific RNA polymerase to the promoter.

Type of Transcription

In eukaryotes, a complex of histone proteins and DNA should be accessible, before the transcription.

In prokaryotic, DNA is not bound to the histone proteins. Therefore, transcription occurs directly.


Eukaryotic DNA that is identified by the RNA polymerase II has two parts of the promoter known as core promoter and regulatory promoter.

 In prokaryotic promoter, no such differentiation can be seen.

Transcription Terminators

Prokaryotic cells possess two types of transcription terminators; Rho-dependent terminators and Rho-independent terminators.

In eukaryotes transcription, the three RNA polymerases use different mechanisms for the termination.

e.g. RNA polymerase I – needs termination factor that binds to the downstream of the DNA termination site.

RNA polymerase II – transcribed the termination sequence and then produces a string of uracils.

Tie to the RNA Molecule

Rho factor binds to the growing RNA molecule in the prokaryotic transcription.

Termination factor in eukaryotes binds to the template DNA molecule.

Enhancement of Proteins

Eukaryotic transcription can be enhanced by proteins called enhancers which are bind to a different place of DNA that is away from the transcribing region.

This is not reported in prokaryotic transcription.Difference Between Prokaryotic and Eukaryotic Transcription - infographic 1

Image Courtesy:

 “Average prokaryote cell- en” by Mariana Ruiz Villarreal, LadyofHats  (Public Domain) via

“Animal cell structure en” by LadyofHats (Mariana Ruiz) – Own work using Adobe Illustrator. Image renamed from Image:Animal cell structure.svg.  (Public Domain) via

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