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Messenger RNA synthesis is a major site for the regulation of gene expression. Eukaryotic messenger RNA synthesis is catalyzed by multisubunit RNA polymerase II (1–3) and proceeds via multiple stages, which are designated preinitiation, initiation, elongation, and termination and which have come to be referred to collectively as the transcription cycle (Fig. 1). The past decade was a watershed for biochemical studies of eukaryotic messenger RNA synthesis. A diverse collection of transcription factors and other nuclear proteins that govern the activity of RNA polymerase II during messenger RNA synthesis was identified and characterized, and unprecedented progress in several key research areas has provided a deeper understanding of the biochemical mechanisms underlying many aspects of eukaryotic transcriptional regulation. First, major breakthroughs in investigations of the structures of eukaryotic protein-coding genes and the role of chromatin in the regulation of their expression were achieved. Chromatin proteins, such as histones and HMG proteins, were found to play crucial roles in gene regulation by packaging genes into inactive or transcriptionally repressed configurations (4–9). Second, many DNA binding transactivators that interact specifically with upstream promoter elements and enhancer sequences located in the promoter-regulatory regions of genes were isolated, classified according to their structures, and found to regulate the expression of specific genes or gene families by controlling the rate of initiation (10) and, as shown more recently, the efficiency of elongation by RNA polymerase II (11–13). Third, chromatin remodeling proteins, such as the multisubunit SWI/SNF (14, 15) and NURF (16, 17) complexes, were discovered and found to play key roles in transcriptional activation by promoting conversion of regions of inactive chromatin into transcriptionally active, open chromatin, thereby allowing DNA binding transactivators and RNA polymerase II access to the promoter-regulatory regions of genes (4, 18–23). Fourth, coactivators, such as the SRB-containing mediator complex (2, 3, 24, 25), CREB binding protein (CBP) 1

Transcription syndromes and the role of RNA polymerase II general transcription factors in human disease.