Table 601

General Transcription Factors Associated with RNA Polymerase II

TBP binds to TATA box, part of TFIID

TFIID includes TBP, recognizes Pol II specific promoter

TFIIA binds upstream of TATA box; required for binding of RNA Pol II to promoter

TFIIB binds downstream of TATA box; required for binding of RNA Pol II to promoter

TFIIF accompanies RNA Pol II as it binds to promoter

TFIIE required for promoter clearance and elongation

TFIIH phosphorylates the tail of RNA Pol II, retained by polymerase during elongation

TFIIJ required for promoter clearance and elongation

In eukaryotes most genes are subject to positive control. Repressors are rare and usually behave differently to those in bacteria.

Common upstream elements include the GC box, CAAT box, API element and Octamer element. The GC box (GGGCGG) is often present in multiple copies. Despite being nonsymmetrical, the GC box works in either orientation and is recognized by the SP1 factor. Some upstream elements are recognized by more than one protein. In these cases, different transcription factors are often present in different tissues. For example, the Oct-1 and Oct-2 proteins both recognize the Octamer element. Oct-1 is found in all tissues but Oct-2 only appears in immune cells, where it helps activate genes encoding antibodies.

The specific transcription factors that bind to the upstream elements and enhancers are thus gene activator proteins. Repressors are rare in eukaryotes. Furthermore, when found, they do not bind to the DNA directly and block the binding of the RNA polymerase. Instead, they bind to some component of the growing transcription apparatus and block further assembly.

Enhancer sequences are located far away from the genes they control.

Enhancers Control Transcription at a Distance

Enhancers are sequences that are involved in gene regulation, especially during development or in different cell types. Enhancers do exactly what their name indicates— they enhance the initiation of transcription as a result of binding specific transcription factors. Enhancers often consist of a cluster of recognition sites and therefore bind several proteins. Some recognition sites (e.g., Octamer and AP1) are found in both enhancers and as upstream elements in promoters.

Although enhancers are sometimes close to the genes they control, more often they are found a considerable distance, perhaps thousands of base pairs away, not even

Enhancers Control Transcription at a Distance 153

Upstream element

TATA box

Initiator box

Gene

Start of transcription

Enhancer

Enhancer

Upstream TATA Start site element box

FIGURE 6.25 Looping Model for Enhancer

Upstream TATA Start site element box

FIGURE 6.25 Looping Model for Enhancer

The enhancer shown here is located downstream of the start site. To enhance transcription, the enhancer first binds several transcription factors. Subsequently, the DNA forms a loop allowing the enhancer to make contact with the transcription apparatus via the bound transcription factors.

associated with the gene. Enhancers may be located either upstream or downstream from the promoter and the position may vary from case to case. In addition, enhancers function equally well in either orientation. Experiments in which enhancers have been moved have shown that an enhancer will increase transcription from any promoter within its neighborhood. These properties imply that the enhancer must make contact with the transcription apparatus. When an enhancer switches a gene on, the DNA between it and the promoter loops out as shown in Figure 6.25.

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