Proc. Natl. Acad. Sci. USA Vol. 94, pp. 15–22, January 1997 Review RNA polymerase II transcription initiation: A structural view D. B. Nikolov*† and S. K. Burley*‡§ *Laboratories of Molecular Biophysics and ‡Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10021 ABSTRACT In eukaryotes, RNA polymerase II tran- constitute another group of DNA targets for factors modu- scribes messenger RNAs and several small nuclear RNAs. Like lating pol II activity. RNA polymerases I and III, polymerase II cannot act alone. Instead, general initiation factors [transcription factor (TF) Transcription Factor IID IIB, TFIID, TFIIE, TFIIF, and TFIIH] assemble on promoter DNA with polymerase II, creating a large multiprotein–DNA In the most general case, messenger RNA production begins complex that supports accurate initiation. Another group of with TFIID recognizing and binding tightly to the TATA accessory factors, transcriptional activators and coactivators, element (Fig. 1). TFIID’s critical role has made it the focus of regulate the rate of RNA synthesis from each gene in response considerable biochemical and genetic study since its discovery to various developmental and environmental signals. Our in human cells in 1980 (7). Our current census of cloned TFIID current knowledge of this complex macromolecular machin- subunits includes more than a dozen distinct polypeptides, ery is reviewed in detail, with particular emphasis on insights ranging in mass from 15 to 250 kDa (reviewed in ref. 8). The gained from structural studies of transcription factors. majority of these TFIID subunits display significant conser- vation among human, Drosophila, and yeast, implying a com- Eukaryotic RNA polymerase II (pol II) is a 12-subunit DNA- mon ancestral TFIID, and gene disruption studies of four yeast dependent RNA polymerase that is responsible for transcrib- TFIID subunits revealed that they are essential for viability (9, ing nuclear genes encoding messenger RNAs and several small 10). nuclear RNAs (1). Despite its obvious structural complexity, DNA binding by human TFIID was first demonstrated with this multisubunit enzyme requires two groups of auxiliary the adenovirus major late promoter (AdMLP) (11). DNase I footprinting studies of the AdMLP and selected human gene proteins to solve two critical biochemical problems. First, pol promoters revealed sequence-specific interactions between II cannot recognize its target promoters directly. Second, pol human TFIID and the TATA element, which are primarily II must be able to modulate production of the RNA transcripts mediated by the TBP subunit of TFIID (see below). In of individual genes in response to developmental and envi- contrast, protection both upstream and downstream of the ronmental signals. TATA element is largely sequence independent, displays a Promoter Anatomy and the Preinitiation Complex (PIC) nucleosome-like pattern of DNase I hypersensitivity, varies radically between promoters, and can be induced by some Class II nuclear gene promoters contain combinations of DNA activators (reviewed in ref. 8). It is remarkable that TATA box sequences, which include core or basal promoter elements, binding by either TFIID or TBP precludes packaging of the promoter proximal elements, and distal enhancer elements. core promoter with the nonlinker histone proteins (H2A, H2B, H3, and H4). Conversely, core promoter packaging by histone Transcription initiation by pol II is precisely regulated by octamers into nucleosomes prevents TFIID or TBP binding to transcription factors (proteins) that interact with these three the TATA element, effectively repressing transcription (re- classes of DNA targets and also with each other (reviewed in viewed in ref. 12). In vivo, chromatin-mediated transcriptional refs. 2–4). The best characterized core promoter elements, repression is overcome by various ATP-dependent macromo- which can function independently or synergistically, are the lecular machines (e.g., the SWI SNF complex) that remodel TATA element (located 25 bp upstream of the transcription y chromatin in the vicinity of the core promoter (reviewed in ref. start site with consensus sequence TATAaytAayt), and a 13). pyrimidine-rich initiator element (located at the start site). The core promoter constitutes the principal DNA target for TATA Box-Binding Protein pol II, and accurate initiation of transcription depends on assembling pol II and transcription factors (TFs) IID, IIB, IIF, Publication of the sequence of yeast TBP in 1989 was followed IIE, and IIH into a PIC (Table 1; Fig. 1). It is believed that rapidly by the sequences of homologous genes from various these transcription factors are required to position pol II on eukaryotes and an archaebacterium (amino acid identities most class II nuclear gene promoters, and they are usually within the phylogenetically conserved 180 residue portion referred to as general initiation factors (reviewed in ref. 2). range between 38% and 100%, reviewed in ref. 14). Recom- Thus, the PIC is functionally equivalent to the much simpler binant TBP alone can bind both general and regulatory factors Escherichia coli holoenzyme, which is composed of the core and direct PIC assembly in vitro and basal transcription RNA polymerase subunits and a s-factor (reviewed in ref. 6). (reviewed in ref. 2). Basal or core promoter-dependent tran- Promoter proximal elements occur anywhere between 50 and scription is a relatively inefficient in vitro reaction that has 200 bp upstream of the start site and transcriptional activators binding to these sequences regulate transcription. Finally, Abbreviations: pol II, polymerase II; PIC, preinitiation complex; distal enhancer elements, which can be found far from the AdMLP, adenovirus major late promoter; cTFIIB, C terminal or core transcription initiation site in either direction and orientation, TFIIB. †Present address: Cellular Biochemistry and Biophysic Program, Me- morial Sloan–Kettering Cancer Center, New York, NY 10021. Copyright q 1997 by THE NATIONAL ACADEMY OF SCIENCES OF THE USA §To whom reprint requests should be addressed at: The Rockefeller 0027-8424y97y9415-8$2.00y0 University, 1230 York Avenue, New York, NY 10021. e-mail: PNAS is available online at http:yywww.pnas.org. [email protected]. 15 Downloaded by guest on September 30, 2021 16 Review: Nikolov and Burley Proc. Natl. Acad. Sci. USA 94 (1997) Table 1. General class II transcription initiation factors from human cells Factor Subunits, kDa (no.) Function TFIID }TBP 38 (1) Binds to TATA, promotes TFIIB binding {TAFs* 15–250 (12) Regulatory functions (1 and 2) TFIIB 35 (1) Promotes TFIIF–pol II binding TFIIF 30, 74 (2) Targets pol II to promoter RNA pol II 10–220 (12) Catalytic function TFIIE 34, 57 (2) Stimulates TFIIH kinase and ATPase activities TFIIH 35–89 (9) Helicase, ATPase, CTD kinase activities All class II GTFs . 2 MDa (.42) Function and subunit composition of the human class II general initiation factors. The factor denoted with an asterisk is not absolutely required for in vitro basal or core promoter-dependent pol II transcription initiation. TBP, TATA box-binding protein; TAF, TBP-associated factor; GTF, general transcription factor. served as an important tool for characterizing pol II’s minimal Watson–Crick base pairing is preserved throughout, and there requirement for TBP, TFIIB, TFIIF, TFIIE, and TFIIH and appears to be no helical strain induced in the DNA because the core region of the promoter immediately upstream of the partial unwinding has been compensated for by right-handed transcription start site. In addition to defining the minimal supercoiling of the double helix. factors required for accurate pol II initiation, the basal tran- DNA packaging into nucleosomes involves wrapping a dou- scription system has been used to establish the order of PIC ble helix around the histone octamer. Sequence-dependent assembly depicted in Fig. 1A. nucleosome positioning correlates with bending A1T-rich Fig. 1B contrasts basal and activated transcription (reviewed sequences toward the minor groove (28, 29), and packaging of in ref. 8). Activated transcription in vivo requires the entire TATA elements into nucleosomes probably results in minor promoter, which includes the core region plus promoter groove compression precluding TBP binding. Conversely, a proximal and distal enhancer regions. Transcriptional activa- preformed PIC remains transcriptionally active after nucleo- tors regulate the efficiency of pol II initiation by recognizing some assembly (30), and recombinant yeast TBP alone pre- their target DNA sequences within promoter proximal or vents nucleosome-mediated repression of transcription (31). distal enhancer elements and interacting with the PIC (pos- Thus, the cocrystal structures of the TBP–DNA complexes sibly via intermediaries known as coactivators). Activated may provide a simple mechanical explanation for the mutual transcription requires TBP and the remaining subunits of exclusion of DNA packaging and transcription. It is widely believed that transcriptional activators bound to promoter TFIID (the TAFIIs), the other general initiation factors TFIIB, TFIIF, TFIIE, and TFIIH, plus transcriptional activators and proximal andyor distal enhancer elements target nucleosome- coactivators. remodeling factors to the core promoters of genes slated for The three-dimensional structure of the conserved portion of expression. Once chromatin has been remodeled, TFIID TBP is strikingly similar to a saddle (14–16) (Fig. 2A),