In genetics, an enhancer is a short region of DNA that can be bound with proteins (namely, the trans-acting factors, much like a set of transcription factors) to enhance transcription levels of genes (hence the name) in a gene-cluster. An enhancer does not need to be particularly close to the genes it acts on, and need not be located on the same chromosome. An enhancer does not need to bind close to the transcription initiation site to affect its transcription, as some have been found to bind several hundred thousand base pairs upstream or downstream of the start site. Enhancers can also be found within introns. An enhancer's orientation may even be reversed without affecting its function. Furthermore, an enhancer may be excised and inserted elsewhere in the chromosome, and still affect gene transcription.That is the reason that intron polymorphisms are checked though they are not transcribed and translated.

Currently, there are two different theories on the information processing that occurs on enhancers:

- Enhanceosomes - rely on highly cooperative, coordinated action and can be disabled by single point mutations that move or remove the binding sites of individual proteins
- Flexible billboards - less integrative, multiple proteins independently regulate gene expression and their sum is read in by the basal transcriptional machinery


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