The Eukaryotic Promoter Region

The promoter is a major regulator of gene expression that contains binding sites for RNA polymerase, the enzyme responsible for transcription, and transcription factors, that facilitate or inhibit the binding of RNA polymerase. 

The promoter region is mostly located upstream of the gene it regulates. It has distinct structural features, such as a curved structure with the ability to bend when transcriptional regulators bind and low thermodynamic stability due to the presence of AT-rich regions.  

In eukaryotes, this transcriptional control region is more complex than in prokaryotes. In addition to the core promoter, eukaryotic genes have many additional cis-regulatory sequences that transcription factors can bind.

Prokaryotic RNA polymerase requires a sigma factor to bind to the promoter, whereas eukaryotic RNA polymerases require several such regulators. 

Additionally, the three different RNA polymerases in eukaryotes that bind to distinct promoters, require different transcriptional regulators. 

The core eukaryotic promoter contains several signature motifs that work together in various combinations to allow RNA polymerase to bind. 

The TATA box is highly conserved across organisms. TATA boxes are usually present in genes that show high levels of cell-specific expression, such as proteins involved in cell differentiation.

Initiator and downstream promoter elements consist of degenerate sequences that follow a specific pattern of nucleotides, though their exact sequence varies.  

The initiator element is the most common promoter motif. It can either help to maintain basal levels of transcription or work together with the TATA box to improve the binding of transcription factors. 

The downstream promoter element is located downstream of the transcription start site and was initially found in promoters lacking a TATA box.  The DPE often works in conjunction with the initiator element to regulate transcription.

CpG islands consist of sections of DNA where a cytosine is followed by a guanine. CpG islands usually regulate housekeeping genes, which are continuously expressed in small amounts and do not require high levels of transcription.