Cis-acting

Cis-regulatory elements (CREs) are regions of non-coding DNA which regulate the transcription of nearby genes. CREs are vital components of genetic regulatory networks, which in turn control morphogenesis, the development of anatomy, and other aspects of developmental biology, now being unified in evo-devo.

CREs are found in the vicinity of the genes that they regulate. CREs typically regulate gene transcription by functioning as binding sites for transcription factors. A single transcription factor may bind to many CREs, and hence control the expression of many genes. The Latin prefix cis means "on this side", i.e. on the same molecule of DNA as the gene(s) to be transcribed. CREs are often but not always upstream of the transcription site.

The genome of an organism contains anywhere from a few hundred to thousands of different genes, all encoding a singular product or more. For numerous reasons, including organizational maintenance, energy conservation, and generating phenotypic variance, it is important that genes are only expressed when they are needed. The most efficient way for an organism to regulate genetic expression is at the transcriptional level. CREs function to control transcription by acting nearby or within a gene. The most well characterized types of CREs are enhancers and promoters. Both of these sequence elements are structural regions of DNA that serve as transcriptional regulators.

Promoters are relatively short sequences of DNA, approximately 40 base pairs (bp), usually located upstream of a transcription start site. This regulatory region includes the site where transcription is initiated and the region approximately 35 bp upstream or downstream from the initiation site. In eukaryotes, promoters usually have the following four components: the TATA box, a TFIIB recognition site, an initiator, and the downstream core promoter element. It has been found that a single gene can contain multiple promoter sites. In order to initiate transcription of the downstream gene, a host of DNA-binding proteins called transcription factors (TFs) must bind sequentially to this region. Only once this region has been bound with the appropriate set of TFs, and in the proper order, can RNA polymerase bind and begin transcribing the gene. Contrastingly, enhancers influence transcription of genes on the same molecule of DNA and can be found upstream, downstream, within the introns, or even relatively far away from the gene they regulate. Multiple enhancers can act in a coordinated fashion to regulate transcription of one gene.

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