In order to discuss how eukaryotic transcription works, it is important to understand that many aspects of this process have evolved from simpler processes in prokaryotic transcription.  Therefore, it is of interest to explain the differences between the two types of transcription.   

In prokaryotic transcription, one RNA polymerase (RNAP) comprised of three subunits (alpha, beta prime, and beta) transcribes all genes without the help of additional protein factors (2).  The selection of the promoter and the control of how much to transcribe is governed by one of more additional proteins.  In contrast, eukaryotic transcription requires three different RNAP’s (I, II, and III) to transcribe three sets of different genes.  RNAPII is the primary focus of this paper as it transcribes mRNA from DNA.  Unlike prokaryotic RNAP, this enzyme requires a whole team of additional protein factors to recognize the promoter and regulate its level of expression.  The greater number of factors and added complexity shows how RNAPII has evolved in eukaryotic organisms. 

In prokaryotes, a protein factor known as σ factor binds to the enzyme and selects where on the DNA transcription will begin (1).  As stated above, eukaryotic RNAPII requires many protein factors, known as transcription factors, to perform the same function.  The eukaryotic transcription factors include: TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH.  Before RNAPII binds to the DNA, transcription factors bind the promoter and recruit the enzyme over to the promoter.  The enzyme and transcription factors form a complex called the pre-initiation complex.  This complex is necessary for the initiation stage of transcription.

In comparison to eukaryotic transcription, the promoter in prokaryotic transcription contains fewer elements for RNAP to recognize and bind to.  Additionally, the location of these elements is also different.  For example, the TATA box in prokaryotes is located at the -10 site of the DNA (2).  For eukaryotes, it is located at the -25 site on the DNA.  Eukaryotic promoters involve additional elements such as upstream activator elements, downstream promoter elements, and initiator sequences. 

Lastly, prokaryotic transcription is coupled with translation (2).  This means, that the mRNA strand synthesized by RNAP is immediately or simultaneously translated once it leaves the enzyme.  This phenomenon occurs, because prokaryotic cells lack membrane-bound nuclei.  However, in eukaryotic transcription, membrane-bound nuclei require the transport of mRNA outside of the nucleus and into the ribosome-containing cytoplasm.  Therefore, mRNA must be further modified before it can be translated in the cytoplasm.