Transcriptional activators are required to turn on the expression of genes in a eukaryotic cell. Activators bound to enhancers stimulate the assembly and activity of the transcription machinery at gene promoters. This article examines selected issues in understanding activator functions and activation mechanisms.


Transcription is the process of copying (transcribing) the information from one strand of DNA into RNA by the enzyme called RNA polymerase (RNAP). In bacteria there is only one RNAP, but in eukaryotes there are three different RNAPs that transcribe different classes of genes (Hahn, 2004). RNAPII is responsible for transcribing protein-coding genes, whereas RNAPI and III are responsible for synthesizing rRNA and tRNA respectively. This article deals with transcription by RNAPII (referred to as RNAP from now on), which has been subject to intensive investigation over the past decades (Kadonaga, 2004; Sims et al., 2004b). A major focus of this article is to discuss mechanisms leading to increased levels of transcription, a process called activation.

In addition to the coding sequence, a typical class II gene contains at least two other types of DNA sequences that are required for initiating transcription. The first such elements are called promoters (also referred to as core promoters). These are specific DNA

sequences located upstream of the coding regions of the genes. Promoters help orient RNAP so that it "knows" where on DNA to start transcribing and in which direction. RNAP itself does not have the ability to recognize specific DNA sequences such as promoters. Instead, a group of proteins, called general transcription factors (GTFs), help RNAP to find promoter sequences (Hampsey, 1998; Orphanides et al., 1996). One of these GTFs is the TATA-box binding protein (TBP), which directly binds to the TATA element of a promoter. The protein complex assembled at the promoter is often referred to as the preinitiation complex or transcription machinery (or apparatus). This complex contains GTFs and RNAP. It also contains co-factors and chromatin modifying/remodeling factors (or complexes) that are part of the RNAP holoenzyme. Many of these additional factors play important roles in mediating transcription regulation by responding to regulatory proteins (Levine and Tjian, 2003; Malik and Roeder, 2000; Naar et al, 2001; Narlikar et al, 2002).

The second type of DNA elements required for initiating gene transcription is the regulatory elements, to which regulatory proteins bind. Those elements that play positive roles in transcription are called upstream activation sequences (UASs) in yeast and enhancers in higher eukaryotes such as humans. These sequences provide the binding sites for transcriptional activators that increase the levels of gene transcription. " Enhancers (and proximal-promoter elements) play particularly important roles in gene expression: genes in eukaryotic cells tend to stay silent (off) unless they are

® For our discussion in this chapter, we treat proximal -promoter elements, which are located immediately upstream of the core promoters, as part of the regulatory elements.

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stimulated (turned on) by activators bound to enhancers. This is obvious for genes that need to be specifically turned on at precise times and locations in response to environmental or developmental signals. This is even true for housekeeping genes that appear to be transcribed at all times; for these genes, their transcription is also dependent on activators bound to regulatory sequences. Many enhancers are located upstream of the genes, but they have also been found in introns or even downstream of the genes. A special feature of enhancers is that they can stimulate transcription in an orientation- and distance- independent manner (Blackwood and Kadonaga, 1998). There are also regulatory elements that play negative roles in transcription; these elements contain binding sites for transcriptional repressors. This article primarily deals with activator functions and mechanisms of activation.

There are several other types of DNA sequences that also play important roles in transcription but are not further discussed in this article. For example, the polyadenylation site located at the end of a gene instructs RNAP to terminate transcription (Ares and Proudfoot, 2005; Tollervey, 2004). In this article we will first discuss how a typical activator looks like and how it might activate transcription. We will then expand our discussion by examining selected issues to further explore activator functions and activation mechanisms.

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