No abstract

Advances in structure determination of the bacterial and eukaryotic transcription machinery have led to a dramatic increase in understanding the mechanism of transcription. Models for the specific assembly of the RNA Polymerase II transcription machinery at a promoter, conformational changes that occur during initiation of transcription, and the mechanism of initiation are discussed in light of recent developments.Regulation of transcription, the synthesis of RNA from a DNA template, is one of the most important steps in control of cell growth and differentiation. Transcription is carried out by the enzyme RNA polymerase (Pol) along with other factors, termed general transcription factors. The general factors are involved in recognition of promoter sequences, the response to regulatory factors, and conformational changes essential to the activity of Pol during the transcription cycle 1,2 . Advances made over the past 11 years 3-5 have revealed the structures of bacterial and eukaryotic Pols, several of the key general transcription factors, and most recently, structures and models for Pol II interacting with general transcription factors 6-8 . Combined with biochemical and genetic studies, these structures provide emerging views on the mechanism of the transcription machinery, the dynamic nature of protein-protein and protein-DNA interactions involved, and the mechanism of transcriptional regulation.While the transcription machinery of eukaryotes is much more complex than that of prokaryotes or archaea, the general principals of transcription and its regulation are conserved. Bacteria and archaea have only one Pol, while eukaryotes utilize three nuclear enzymes, Pol I, II, and III, to synthesize different classes of RNA. The nuclear Pols share five common subunits, with the remainder showing strong similarity among the eukaryotic and archaeal enzymes 2,9 . Although these enzymes have many more subunits than bacterial Pol, subunits that comprise most of Pol II are homologous to subunits from all cellular Pols, implying that all these enzymes have the same basic structure and mechanism 10 . In bacteria, the sigma subunit is the sole general transcription factor-like polypeptide. Sigma recognizes promoter sequences, promotes conformational changes in the Pol-DNA complex upon initiation, and interacts directly with some transcription activators. In eukaryotes, sigma factor function has been replaced by a much larger set of polypeptides, with each of the three forms of Pol having their own set of associated general transcription factors 2,11,12 . The Pol II transcription machinery is the most complex, with a total of nearly 60 polypeptides (Table 1), only a few of which are required for transcription by the other nuclear Pols. In contrast, archaea utilize a simplified version of a Pol II/Pol III-like system, relying on only two essential general, factors, TBP (TATA binding protein), and TFB (related to the Pol II and Pol III general factors TFIIB and Brf1) 9 .Correspondence should be addressed to shahn@fhcrc....

High levels of gene transcription by RNA polymerase II depend on high rates of transcription initiation and reinitiation. Initiation requires recruitment of the complete transcription machinery to a promoter, a process facilitated by activators and chromatin remodelling factors. Reinitiation probably occurs through a different pathway. After initiation, a subset of the transcription machinery remains at the promoter, forming a platform for assembly of a second transcription complex. Here we describe the isolation of a reinitiation intermediate that includes transcription factors TFIID, TFIIA, TFIIH, TFIIE and Mediator. This intermediate can act as a scaffold for formation of a functional reinitiation complex. Formation of this scaffold is dependent on ATP and TFIIH. The scaffold is stabilized in the presence of the activator Gal4-VP16, but not Gal4-AH, suggesting a new role for some activators and Mediator in promoting high levels of transcription.