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A proximal promoter is a region in Deoxyribonucleic acid (DNA) just before the beginning of a gene where proteins and other molecules bind in preparation to read that gene. The promoter region is essential for most genes to be read and transcribed into protein, in both simple prokaryotic cells and the more complex eukaryotes. A variety of proteins called transcription factors bind to the DNA in this region, and they perform many tasks preparing for gene transcription. The most important of these functions is building a scaffold of proteins that holds the DNA open and transcribes the proper gene at the same time.
The exact location and structure of a proximal promoter varies between genes and cell types. Prokaryotic cells, those with no nucleus, usually have one type of promoter while eukaryotic cells, those with a true nucleus, have another. Promoters usually lie a few nucleotides upstream of, or before, the gene that they control. Almost every promoter contains a special sequence of nucleotides that identifies it as such. In general, prokaryotic promoters are identified by a group of nucleotides called the Shine-Dalgarno sequence, and eukaryotic promoters are identified by a specific genetic sequence called the TATA box.
Despite these relatively simple rules, not every proximal promoter follows them, which can make identifying them, and the genes they control, somewhat difficult. The distance between a promoter and its gene is not fixed within a species or within a single organism, so determining where they sit in relation to each other is not trivial. Proximal promoter sequence compositions are not always identical; they may very in length, composition, or both. In addition, the marker sequences of the Shine-Dalgarno box or TATA box have some variability in them. How the varied transcription factors recognize promoters in the face of this inherent variability is not easy to determine, and new examples appear frequently that call into question these previously robust solutions.
When a gene is very close to another gene, the possibility exists that its proximal promoter could be affected by the action of the nearby gene. Sometimes, this is done purposely in the genome, perhaps to stimulate multiple genes at once or regulate their action simultaneously. At other times, a connection between two genes through a promoter's activity is done in error. To prevent this cross-talk between genes where it isn't warranted, some genomes have insulator regions between them. This extra region isn't always necessary, and some genomes prevent cross-talk by gene positioning in other ways, like forcing one gene to be inactive while another is active.
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