Transcription is an important level of control in eukaryotic cells, and this control requires a number of different types of proteins and regulatory elements. Eukaryotic promoters for genes that encode proteins consist of two parts: a core promoter, which is located immediately upstream of the gene, and a regulatory promoter, which lies upstream of the core promoter. Proteins called general transcription factors and RNA polymerase assemble into a basal transcription apparatus, which binds to a core promoter. The basal transcription apparatus is capable of minimal levels of transcription, but transcriptional regulator proteins are required to bring about normal levels of transcription. These proteins bind to the regulatory promoter and affect the levels of transcription that take place (Figure 12.16). Transcriptional regulator proteins also bind to enhancers, which are regulatory elements that may be located some distance from the gene. The exact position and orientation of an enhancer in relation to the promoter it affects can vary. Some transcriptional regulator proteins are activators; others are repressors.

TRANSCRIPTIONAL ACTIVATORS AND REPRESSORS Transcriptional activator proteins stimulate and stabilize the basal transcription apparatus at the core promoter. The activators may interact directly with the basal transcription apparatus or indirectly through protein coactivators. Some activators and coactivators, as well as general transcription factors, also have acetyltransferase activity and so further stimulate transcription by altering chromatin structure. Some regulatory proteins in eukaryotic cells act as repressors, inhibiting transcription. These repressors bind to sequences in the regulatory promoter or to silencers. Silencers, like enhancers, affect transcription at distant promoters and are position and orientation independent. Unlike repressors in bacteria, most eukaryotic repressors do not directly block RNA polymerase. These repressors may compete with transcriptional activators for DNA binding sites: when a site is occupied by an activator, transcription is activated, but if a repressor occupies that site, there is no activation. Alternatively, a repressor may bind to sites near an activator-binding site and prevent the activator from contacting the basal transcription apparatus. A third mechanism of repressor action is direct interference with the assembly of the basal transcription appa­ratus, which blocks the initiation of transcription.

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Within the regulatory promoter are typically several different consensus sequences to which different transcriptional activators and repressors can bind. Among different promoters, these binding sites are mixed and matched in different combinations (Figure 12.17), so each promoter is regulated by a unique combination of transcriptional activator and repressor proteins.

ENHANCERS AND INSULATORS Enhancers are capable of affecting transcription at distant promoters. For example, an enhancer that regulates the gene encoding the alpha chain of the T-cell (T-lymphocyte) receptor is located 69,000 bp downstream of the gene’s promoter. Furthermore, the exact position and orientation of an enhancer relative to that of the promoter is not critical to its function. How can an enhancer affect the initiation of transcription at a promoter that is tens of thousands of base pairs away? In many cases, transcriptional regulator proteins bind to the enhancer and cause the DNA between the enhancer and the promoter to loop out, bringing the promoter and enhancer close to each other, so that the transcriptional regulator proteins are able to interact directly with the basal transcription apparatus at the core promoter (see Figure 12.16).

Recent research demonstrates that many enhancers are themselves transcribed into short RNA molecules called enhancer RNAs (eRNAs). Evidence suggests that transcription of enhancers is often associated with transcription at the promoters that the enhancers affect. How transcription at the enhancer might affect transcription occurring at a distant promoter is not clear. The enhancer might recruit RNA polymerase, which might then be transferred to the promoter when the enhancer interacts with the promoter. Alternatively, transcription of the enhancer might allow the chromatin to adopt a more open configuration, which would then facilitate transcription at nearby promoters.

Most enhancers are capable of stimulating any promoter in their vicinities. Their effects are limited, however, by insulators (also called boundary elements), which are DNA sequences that block or insulate the effects of enhancers in a position-dependent manner. If the insulator lies between the enhancer and the promoter, it blocks the action of the enhancer, but if the insulator lies outside the region between the two, it has no effect (Figure 12.18). Specific proteins bind to insulators and play a role in their blocking activity. Some insulators also limit the spread of changes in chromatin structure that affect transcription. Some enhancer-like elements are found in prokaryotes. TRY PROBLEM 34

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COORDINATED GENE REGULATION Although most eukaryotic cells do not possess operons, several eukaryotic genes may be activated by the same stimulus. For example, many eukaryotic cells respond to extreme heat and other stresses by producing heat-shock proteins, which help to prevent damage from such stressing agents. Heat-shock proteins are produced by a large number of different genes. During times of environmental stress, transcription of all the heat-shock genes is greatly elevated. Groups of bacterial genes are often coordinately expressed (turned on and off together) because they are physically clustered as an operon and have the same promoter, but coordinately expressed genes in eukaryotic cells are not clustered. How, then, is the transcription of eukaryotic genes coordinated if they are not organized into an operon?

Genes that are coordinately expressed in eukaryotic cells are able to respond to the same stimulus because they share short regulatory sequences in their promoters or enhancers. For example, different eukaryotic heat-shock genes possess a common regulatory element upstream of their start sites. Such DNA regulatory sequences are called response elements; they typically contain the same short consensus sequences at varying distances from the gene being regulated. The response elements are binding sites for transcriptional activators, which bind to the response elements and elevate transcription.