▪ Abstract The events leading to transcription of eukaryotic protein-coding genes culminate in the positioning of RNA polymerase II at the correct initiation site. The core promoter, which can extend ∼35 bp upstream and/or downstream of this site, plays a central role in regulating initiation. Specific DNA elements within the core promoter bind the factors that nucleate the assembly of a functional preinitiation complex and integrate stimulatory and repressive signals from factors bound at distal sites. Although core promoter structure was originally thought to be invariant, a remarkable degree of diversity has become apparent. This article reviews the structural and functional diversity of the RNA polymerase II core promoter.

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The RNA polymerase II core promoter.

Targeted Recruitment of Set1 Histone Methylase by Elongating Pol II Provides a Localized Mark and Memory of Recent Transcriptional Activity

In eukaryotes, the core promoter serves as a platform for the assembly of transcription preinitiation complex (PIC) that includes TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, and RNA polymerase II (pol II), which function collectively to specify the transcription start site. PIC formation usually begins with TFIID binding to the TATA box, initiator, and/or downstream promoter element (DPE) found in most core promoters, followed by the entry of other general transcription factors (GTFs) and pol II through either a sequential assembly or a preassembled pol II holoenzyme pathway. Formation of this promoter-bound complex is sufficient for a basal level of transcription. However, for activator-dependent (or regulated) transcription, general cofactors are often required to transmit regulatory signals between gene-specific activators and the general transcription machinery. Three classes of general cofactors, including TBP-associated factors (TAFs), Mediator, and upstream stimulatory activity (USA)-derived positive cofactors (PC1/PARP-1, PC2, PC3/DNA topoisomerase I, and PC4) and negative cofactor 1 (NC1/HMGB1), normally function independently or in combination to fine-tune the promoter activity in a gene-specific or cell-type-specific manner. In addition, other cofactors, such as TAF1, BTAF1, and negative cofactor 2 (NC2), can also modulate TBP or TFIID binding to the core promoter. In general, these cofactors are capable of repressing basal transcription when activators are absent and stimulating transcription in the presence of activators. Here we review the roles of these cofactors and GTFs, as well as TBP-related factors (TRFs), TAF-containing complexes (TFTC, SAGA, SLIK/SALSA, STAGA, and PRC1) and TAF variants, in pol II-mediated transcription, with emphasis on the events occurring after the chromatin has been remodeled but prior to the formation of the first phosphodiester bond.

The general transcription machinery and general cofactors.

Identification and Distinct Regulation of Yeast TATA Box-Containing Genes

The development, growth, and survival of eukaryotic organisms require the proper regulation of tens of thousands of genes. By complex formulae that have yet to be solved, the expression of each of these thousands of genes is controlled by a wide variety of mechanisms (e.g., see Lefstin and Yamamoto 1998; Roeder 1998; Struhl 1999; Glass and Rosenfeld 2000; Lee and Young 2000; Lemon and Tjian 2000; Strahl and Allis 2000; Courey and Jia 2001; Smale 2001; White 2001; Zhang and Reinberg 2001; Emerson 2002; McKenna and O’Malley 2002; Narlikar et al. 2002; Orphanides and Reinberg 2002; West et al. 2002). In this review, we will focus on one of these regulatory components—the RNA polymerase II core promoter.

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The RNA polymerase II core promoter: a key component in the regulation of gene expression.

Transcriptional activity in yeast strongly correlates with promoter occupancy by general factors such as TATA binding protein (TBP), TFIIA, and TFIIB, but not with occupancy by TBP-associated factors (TAFs). Thus, TBP exists in at least two transcriptionally active forms in vivo. The TAF-containing form corresponds to the TFIID complex, whereas the form lacking TAFs corresponds to TBP itself or to some other TBP complex. Heat shock treatment altered the relative utilization of these TBP forms, with TFIID being favored. Promoter-specific variations in the association of these distinct forms of TBP may explain why only some yeast genes require TFIID for transcriptional activity in vivo.

https://struhl.med.harvard.edu/sites/struhl.med.harvard.edu/files/publications/Publications2000/kuras%20et%20al,%202000%20science.pdf

TAF-Containing and TAF-independent forms of transcriptionally active TBP in vivo.

We have made a DNA microarray that includes not only all the open reading frames (ORFs) and other features in the yeast genome, but also all the intergenic regions. We are using this as a tool to construct genome-wide maps of DNA-protein interactions for proteins that interact directly or indirectly with DNA or chromatin in vivo. Proteins are crosslinked to DNA in vivo using formaldehyde and the crosslinked DNA is extracted and sheared. DNA specifically associated with any protein of interest is immunoprecipitated using a specific antibody against the protein or an epitope tag that may be fused to the protein. The selected DNA, representing loci that the protein interacts with in vivo, can be identified by fluorescently labelling it and hybridizing it to the microarray along with an appropriate reference probe. This approach is being used to map the genome-wide interactions of sequence-specific DNA binding proteins, components of the transcription machinery and chromatin components, under a variety of conditions.

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Peter Kosa

Papers

TAF-Containing and TAF-independent forms of transcriptionally active TBP in vivo.

Genome-wide maps of DNA-protein interactions using a yeast ORF and intergenic microarray