Transcription Initiation: a Complex Game with Many Players

Transcription of eukaryotic genes is a complex process requiring the action of a myriad of proteins. Central to the process is the large multi-subunit enzyme RNA polymerase II (Pol II), which contains 12 subunits (Lewin, 1997). In spite of its complexity, Pol II requires a series of general transcription factors (GTFs) to recognize, bind, and clear the core promoter of each gene. These GTFs are TFIID, TFIIA, TFIIB, TFIIE, TFIIF and TFIIH (Conway and Conway, 1993; Maldonado and Reinberg, 1995) (Fig. 1). Regulation of gene transcription occurs at all stages, initiation, elongation and termination. Control of transcription at the initiation stage relies on the existence of multiple specific sequences that have regulatory duties. In front of the start of the coding region is the core promoter of the gene, the place where the transcriptional machinery assembles. In addition, there are enhancer and silencer sequences, sometimes far from the coding region, to which activators and repressors bind and, respectively, facilitate and inhibit the transcription of a gene. In the absence of activators bound to enhancer elements, the core transcription complex made up of the six GTFs and Pol II can accurately initiate basal levels of RNA synthesis in vitro. In the presence of gene-selective enhancerand promoter-binding activators, significantly elevated levels of transcription initiation can be achieved (Zawel and Reinberg, 1995). This gene-specific regulation is thought to be fine-tuned by the synergistic effect of several activators/repressors acting simultaneously. One current view of mammalian gene regulation is that activators stimulate transcription largely by promoting assembly of the general transcriptional machinery at the core promoter (Ptashne and Gann, 1997). Alternatively, activators could have a direct effect on the conformation of some of the GTFs and/or DNA structure (Chi and Carey, 1996; Roberts and Green, 1994). As Pol II escapes from the promoter and elongates through the gene, it allows the entrance of another polymerase so that multiple mRNAs can be produced. Some studies support the idea that a major effect of activators is to stimulate promoter escape (Sandaltzopoulos and Becker, 1998). Of the six essential GTFs mentioned above, TFIID, which contains the TATA-binding protein (TBP), is the first to bind to the core promoter and to facilitate the assembly of the complete initiation machinery. In addition to TBP, TFIID contains up to 12 other proteins, TBP-associated factors (TAFs), which are involved in the recognition of promoter elements other than the TATA box and are important for the regulation of the general machinery by activators (Goodrich and Tjian, 1994). In the current model of initiation machinery assembly, TFIIA and TFIIB contact DNA and TBP, increasing the stability of TBP binding. Then a complex of TFIIF–Pol-II is recruited, followed by TFIIE and TFIIH. TFIIH is required to melt the DNA at the start site and for Pol II to clear the promoter and initiate transcription. Although this is a generally accepted model, the order of assembly, and the stability of any intermediate complex bound or unbound to DNA, still needs direct structural confirmation. An alternative model is that the general machinery assembles in solution and binds to the DNA 4391 Journal of Cell Science 113, 4391-4397 (2000) Printed in Great Britain © The Company of Biologists Limited 2000 JCS1484