The proteins mentioned in the previous section are termed basal factors. They are required on all promoters and constitute a core of the transcription activity. Additionally, eukaryotic promoters often also possess one or more 8-to-30 base-pair elements located 100 to 10,000 base pairs upstream or downstream from the transcription start point. Similar elements are found with prokaryotic promoters, but less frequently. These elements enhance the promoter activity by five to a thousand-fold. They were first found in animal viruses, but since then have been found to be associated with nearly all eukaryotic promoters. The term, enhancer, is shifting slightly in meaning. Originally it meant a sequence possessing such enhancing properties. As these enhancers were dissected, frequently they were found to possess binding sites for not just one, but sometimes up to five different proteins. Each of the proteins can possess enhancing activity, and now the term enhancer can mean just the binding site for a single enhancer protein.

Remarkably, enhancer elements still function when their distances to the promoter are altered, and frequently they retain activity when the enhancers are turned around, or even when they are placed downstream from the promoter. Proteins bound to the enhancer sequences must communicate with the RNA polymerase or other proteins at the promoter. There are two ways this can be done, either by sending signals along the DNA between the two sites as was first suggested, or by looping the DNA to permit the two proteins to interact directly (Fig. 1). Most of the existing data favor looping as the method of communication between most enhancers and their associated promoter.

Fig1. How DNA looping permits a protein bound to DNA to contact an initiation complex bound hundreds of nucleotides away.

A second remarkable property of enhancers is their interchangeability. Enhancers frequently confer the appropriate regulation properties on multiple promoters. That is, an enhancer-binding protein senses the cellular conditions and then stimulates appropriately whatever promoter is nearby. Enhancers confer specific responses that are sensitive to tissue-type, developmental stage, and environmental conditions. For example, when an enhancer that provides for steroid-specific response of a gene is placed in front of another gene and its promoter, the second gene acquires a steroid-specific response. That is, enhancers are general modulators of promoter activity, and in most cases a specific enhancer need not be connected to a specific promoter. Most enhancers are able to function in association with almost any promoter. Not surprisingly, a promoter that must function in many tissues, for example, the promoter of a virus that grows in many tissues, has many different enhancers associated with it.