Eukaryotic structure and function are known to be more complex than that of prokaryotes, so it is understandable that the transcription process is also more complex. One main difference is that eukaryotes have three enzymes (polymerase I-III) that are used to synthesize different classes of RNA, whereas prokaryotes only require one enzyme.

Prokaryotic polymerase consists of a smaller number of subunits, in which the alpha-subunit is the sole transcription “factor-like” enzyme. The alpha-subunit is the only factor that promotes initiation and interacts with the DNA complex. As shown in the description of eukaryotic transcription, there are several factors that are involved in transcription; furthermore, each kind of RNA class may require different flavors of these transcription factors.

Also, in eukaryotes, transcription is the initial step in gene replication in which after the mRNA is formed it travels into the cytoplasm of the cell and begins the translation process.  In prokaryotes, transcription and translation happens simultaneously within the cytoplasm.  This is due to the un-complex nature of the prokaryotic organism.

Finally, in eukaryotic transcription, on the mRNA one gene is usually represented by only one protein, whereas in prokaryotic transcription proteins on the mRNA strand can mean more than one gene.