The Promoter:
The open reading frame (ORF) is the region of DNA that is actively transcribed by RNA polymerase II. The promoter is the region of DNA that precedes (or is upstream from) the ORF. This region is necessary for RNA polymerase II to recognize and bind to during the formation of the pre-initiator complex. The promoter contains two types of elements: core promoter elements and upstream promoter elements. The core promoter elements include the TATA box, initiators, and downstream promoter elements. All of these elements influence transcription but may not be present in all organisms.
The TATA box is an evolutionarily conserved A-T-rich region of DNA located 25-30 nucleotides upstream from the start site in complex eukaryotic organisms (3). In yeast, this location varies from 40-120 nucleotides upstream from the start site. In mutant organisms with particular genes that contain deletions of the TATA-box region, transcription initiation of those genes took place 30 nucleotides downstream of the start site. This indicates that RNA polymerase relies on the TATA-box for recognition of and binding to a narrow area on the DNA. However, it should be noted that not all actively transcribed genes contain a TATA-box.
Initiators (Inrs) are conserved sequences that surround the start site of some organisms (4). These sequences direct RNA polymerase to the start site and ensure basal levels of transcription even in the absence of the TATA box and upstream promoter elements. However, in presence of such additional promoter elements, initiators greatly increase the level of transcription.
Downstream promoter elements (DPE’s) are regulatory promoter elements that work together with Inr’s in organisms that lack the TATA box (5). Drosophila or fruit flies are a common example of such organisms that contain DPE’s. Similar to the function of the TATA box, DPE’s RNA polymerase II recognize the promoter and they ensure the efficiency of transcription.
Upstream elements (activators) ensure transcriptional efficiency of RNA polymerase (4). In some eukaryotic organisms, for example, G-C rich regions have been found approximately 47 to 61 and 80 to 105 upstream from the start site. These regions, also called GC boxes, are known to increase the level of transcription compared to organisms lacking such regions.