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A preassembled holoenzyme consisting of RNA polymerase,.

Transcription start a

.transcription factors, and the mediator binds to TFIID.

Transcription activator proteins bind to sequences in enhancers.

.transcription factors, and the mediator binds to TFIID.

Transcription activator proteins bind to sequences in enhancers.

Enhancer

| DNA loops out, allowing the proteins bound to the enhancer to interact with the basal transcription apparatus.

Coactivator

Enhancer

| DNA loops out, allowing the proteins bound to the enhancer to interact with the basal transcription apparatus.

Coactivator

Transcriptional activator protein

Transcriptional activator protein

Transcriptional activator protein

Transcriptional activator protein

^Transcription activator proteins bind to sequences in the regulatory promoter and interact with the basal transcription apparatus through the mediator.

Basal transcription apparatus

113.17 Transcription is initiated at RNA polymerase II promoters when the TFIID transcription factor binds to the TATA box, followed by the binding of a preassembled holoenzyme containing general transcription factors, RNA polymerase II, and the mediator.

I 13.18 The TATA-binding protein (TBP) binds to the minor groove of DNA, straddling the double helix of DNA like a saddle.

combine with TBP to form the complete TFIID transcription factor.

The large holoenzyme consisting of RNA polymerase, additional transcription factors, and the mediator are thought to preassemble and bind as a unit to TFIID. The other transcription factors provide additional functions: TFIIA helps to stabilize the interaction between TBP and DNA, TFIIB plays a role in the selection of the start site, and TFIIH has helicase activity and unwinds the DNA during transcription. The mediator plays a role in communication between the basal transcription apparatus and transcrip-tional activator proteins (see next subsection).

Regulatory promoter The regulatory promoter is located immediately upstream of the core promoter. A variety of different consensus sequences may be found in the regulatory promoters, and they can be mixed and matched in different combinations (IFigure 13.19). Transcriptional activator proteins bind to these sequences and, either directly or indirectly (through the mediation of coactivator proteins), make contact with the mediator in the basal transcription apparatus and affect the rate at which transcription is initiated. Some regulatory promoters also contain repressing sequences, which are bound by proteins that lower the rate of transcription through inhibitory inactions with the mediator.

Enhancers DNA sequences that increase the rate of transcription at distant genes are called enhancers. Furthermore, the precise position of an enhancer relative to a gene's transcriptional start site is not critical; most enhancers can stimulate any promoter in their vicinities, and an enhancer may be upstream or downstream from the affected gene or, in some cases, within an intron of the gene itself.

Enhancers also contain sequences that are recognized by transcriptional activator proteins. How does the binding of a transcriptional activator protein to an enhancer affect the initiation of transcription at a gene thousands of nucleotides away? The answer is that the DNA between the enhancer and the promoter loops out, allowing the enhancer and the promoter to lie close to each other. Tran-scriptional activator proteins bound to the enhancer interact with proteins bound to the promoter and stimulate the transcription of the adjacent gene (see Figure 13.17). The looping of DNA between the enhancer and the promoter explains how the position of an enhancer can vary with regard to the start site—enhancers that are farther from the start site simply cause a longer length of DNA to loop out.

Sequences having many of the properties possessed by enhancers sometimes take part in repressing transcription instead of enhancing it; such sequences are called silencers. Although enhancers and silencers are characteristic of eukaryotic DNA, some enhancer-like sequences have been found in bacterial cells.

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