New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB

Abstract

A sequence element located immediately upstream of the TATA element, and having the consensus sequence 5-G/C-G/C-G/A-C-G-C-C-3, affects the ability of transcription factor IIB to enter transcription complexes and support transcription initiation. The sequence element is recognized directly by the transcription factor IIB. Recognition involves ␣-helices 4 and 5 of IIB, which comprise a helix-turn-helix DNA-binding motif. These observations establish that transcription initiation involves a fourth core promoter element, the IIB recognition element (BRE), in addition to the TATA element, the initiator element, and the downstream promoter element, and involves a second sequence-specific general transcription factor, IIB, in addition to transcription factor IID. Efficient transcription initiation at a human protein-encoding gene requires assembly on promoter DNA of a multiprotein complex containing RNA polymerase II (Pol II) and six general transcription factors, IIA, IIB, IID, IIE, IIF, and IIH (for review, see Orphanides et al. 1996;Roeder 1996;Nikolov and Burley 1997). Previous work establishes that assembly of the complex involves three core promoter elements: (1) the TATA element, located near position −30, (2) the initiator element, located near position −1, and (3) the downstream promoter element, located near position +30 (Burke and Kadonaga 1996;Orphanides et al. 1996;Roeder 1996). Transcription factor IID is responsible for recognition of at least two of these elements. One subunit of IID, TATA-binding protein (TBP), is responsible for recognition of the TATA element; one or more of the remaining subunits of IID, TBP-associated factors (TAFs), is responsible for recognition of the downstream promoter element. It is not clear which factor is responsible for recognition of the initiator element.The crystallographic structure of a ternary complex of transcription factor IIB core domain (IIBc), TBP core domain (TBPc), and a 16-bp DNA fragment containing the TATA element shows that IIBc interacts with both TBPc and DNA, interacting with the DNA major groove immediately upstream of the TATA element and the DNA minor groove immediately downstream of the TATA element ( Fig. 1; Nikolov et al. 1995). In the crystallographic structure, details of the interaction between IIBc and the DNA major groove upstream of the TATA element are incomplete, since the structure was determined using a DNA fragment containing only three nucleotide pairs upstream of the TATA element (Nikolov et al. 1995). However, DNA-binding and site-specific protein-DNA photocross-linking experiments confirm that interaction between IIB and the DNA major groove upstream of the TATA element occurs and indicate that the interaction is extensive, spanning up to 7-9 nucleotide pairs (Lee and Hahn 1995;Lagrange et al. 1996). The observation that IIB makes extensive interactions with the DNA major groove upstream of the TATA element raises the possibility that the ability of IIB to enter into transcription complexes and, thus, the ability of IIB to support...

Nuclear Import of TFIIB Is Mediated by Kap114p, a Karyopherin with Multiple Cargo-binding Domains

“…Sua7p can bind directly to Kap114p, likely via the Sua7p core domain, which is necessary and sufficient for import. The core domain of Sua7p is also necessary for interaction with TBP and with DNA at the promoter of RNAP II encoded genes (Bagby et al, 1995;Nikolov et al, 1995;Lagrange et al, 1998). Because Sua7p can interact with TBP in cytosol and TBP is itself a cargo for Kap114p, this raised the possibility that both Sua7p and TBP can be imported together as a complex by Kap114p.…”

“…The core domain consists of two alpha helical repeats that interact with TBP and promoter DNA (Bagby et al, 1995;Nikolov et al, 1995;Lagrange et al, 1998). We attempted to map the NLS of Sua7p by creating GFP fusions of different domains of Sua7p and determining which domain was sufficient to direct nuclear localization of the fusion.…”

The DPE, a core promoter element for transcription by RNA polymerase II

“…The consensus sequence for the BRE is G/C-G/C-G/A-C-G-C-C, where the 3' C of the BRE is immediately followed by the 5' T of the TATA box. In the analysis of 315 TATA-containing promoters, a motif with at least a 5 out of 7 match with the BRE consensus was found in 12% of the promoters (Lagrange et al, 1998). Under different experimental conditions, the BRE has been found to exhibit both positive and negative effects upon transcriptional activity (Lagrange et al, 1998;Evans et al, 2001).…”

“…A subset of TATA boxes possess an upstream sequence termed the BRE, which is a recognition site for the binding of TFIIB (Lagrange et al, 1998). The consensus sequence for the BRE is G/C-G/C-G/A-C-G-C-C, where the 3' C of the BRE is immediately followed by the 5' T of the TATA box.…”

TRF2: TRansForming the view of general transcription factors

“…The BRE u is located immediately upstream of the TATA box (with a SSRCGCC consensus sequence), and the BRE d is located immediately downstream of the TATA box (with a RTDKKKK consensus sequence). [16][17][18] The initiator (Inr) is the most commonly occurring motif among core promoter elements. [12][13][14][15]19 The Inr encompasses the TSS 20 and its consensus is YYANWYY in humans and TCAKTY in Drosophila.…”