Eukaryotic Transcription:

            Initiation of transcription in eukaryotic cells is mediated by the recognition of the TATA box, located -35 base pairs upstream from the start site. The recognition of this position is thought to be mediated by the transcription factor TFIIB and TFIIF (Conaway and Conaway, 1991). These transcription factors can be stimulated by other transcription factors to bind to the TATA box. Once these proteins bind to the TATA box, the RNA Polymerase II is able to bind to the two transcription factors, forming the initiation complex. This complex is then joined by a number of other transcription factors that aid in the elongation and eventual termination of transcription. Before elongation can begin, the RNA Polymerase II carboxyl-terminal domain (CTD) needs to be phosphorylized. Once phosphorylated, RNA Polymerase II initiation complex is then able to move from the TATA box to the initiation site, unwind the DNA double helix about 10-20 base pairs, and begin transcription. This phosphorylated form of RNA Polymerase II, along with the other transcription factors, forms the elongation complex (Kerppola and Kane, 1991). Elongation continues until the elongation complex reaches the termination site, which is indicated by a specific sequence, as in the TATA box is for initiation. At the termination site, the transcription complex dissociates, the RNA Polymerase II becomes dephosphorylated, and all the factors involved in transcription are ready to transcribe another gene.

Prokaryotic Transcription:

            The initiation of transcription in prokaryotic cells is mediated by proteins called σ factors and their recognition of specific promoters. Once the σ factors have recognized and bound to the promoter region, which is located at -35 and -10 base pairs upstream from the start site, prokaryotic RNA Polymerase is then able to bind to the DNA. At this point, other transcription factors, similar to those found in eukaryotes, are then able to bind to the RNA Polymerase initiation complex (Helmann and Chamberlin, 1988). The elongation process in prokaryotes is similar to that in eukaryotes. However, the termination is vastly different. There are two forms of prokaryotic termination: rho-dependent and rho-independent. In rho-dependent termination, a protein, called the rho factor, binds as a hexamer to the growing mRNA strand and makes its way up to the elongation complex. When the hexamer reaches the complex, it causes an A-T rich region (A-U on the mRNA strand) to form a hairpin loop, causing the elongation complex to stall and terminate transcription. In the rho-independent termination, the A-T rich region of the DNA is long enough to stimulate the formation of the hairpin loop by itself. Upon the formation of the hairpin loop, the elongation complex stalls and terminates transcription (Kerppola and Kane, 1991; Henkin, 1996)

Main Differences

As I have implied above, there are some subtle differences between prokaryotic and eukaryotic transcription. Prokaryotes only have one RNA Polymerase, whereas eukaryotes have three, with the RNA Polymerase II being homologous to the prokaryotic RNA Polymerase. The transcription factors that initiate transcription are also slightly different; prokaryotes have sigma factors while eukaryotes have general and specific transcription factors. The elongation process, however, is conserved between the two groups. Termination for prokaryotes is determined by a hairpin loop whereas eukaryotes depend primarily on termination elements that are located about 500bp downstream of the poly(A) site. The termination of transcription is the most unique difference between the two groups. The most essential difference between eukaryotic and prokaryotic transcription is that eukaryotic transcription occurs within the nucleus whereas prokaryotic transcription occurs in the cytoplasm.