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As promoters are typically immediately adjacent to the gene in question, positions in the promoter are designated relative to the transcriptional start site, where transcription of DNA begins for a particular gene (i.e., positions upstream are negative numbers counting back from -1, for example -100 is a position 100 base pairs upstream).
Promoter activity is a term that encompasses several meanings around the process of gene expression from regulatory sequences —promoters [2] and enhancers. [3] Gene expression has been commonly characterized as a measure of how much, how fast, when and where this process happens. [ 4 ]
The promoter is located at the 5' end of the gene and is composed of a core promoter sequence and a proximal promoter sequence. The core promoter marks the start site for transcription by binding RNA polymerase and other proteins necessary for copying DNA to RNA.
[2] [3] If the regulatory sequence is located far away, the DNA will loop over itself (DNA looping) in order for the bound activator to interact with the transcription machinery at the promoter site. [2] [3] In prokaryotes, multiple genes can be transcribed together , and are thus controlled under the same regulatory sequence. [2]
Enhancers are DNA sequences found in 5′ flanking regions of eukaryotic genes that affect transcription. If a transcription factor binds to an enhancer in a 5′ flanking region, the DNA strand bends in a way that the transcription factor that is bound to the enhancer can also bind the promoter of a gene.
Cis-regulatory DNA sequences that are located in DNA regions distant from the promoters of genes can have very large effects on gene expression, with some genes undergoing up to 100-fold increased expression due to such a cis-regulatory sequence. [3] These cis-regulatory sequences include enhancers, silencers, insulators and tethering elements. [4]
A gene can have more than one promoter, resulting in messenger RNAs that differ in how far they extend in the 5' end. [58] Highly transcribed genes have "strong" promoter sequences that form strong associations with transcription factors, thereby initiating transcription at a high rate.
Reporter genes can be used to assay for the activity of a particular promoter in a cell or organism. [23] In this case there is no separate "gene of interest"; the reporter gene is simply placed under the control of the target promoter and the reporter gene product's activity is quantitatively measured.