Core Promoter Binding by Histone-Like TAF Complexes

Abstract

A major function of TFIID is core promoter recognition. TFIID consists of TATA-binding protein (TBP) and 14 TBP-associated factors (TAFs). Most of them contain a histone fold domain (HFD) that lacks the DNAcontacting residues of histones. Whether and how TAF HFDs contribute to core promoter DNA binding are yet unresolved. Here we examined the DNA binding activity of TAF9, TAF6, TAF4b, and TAF12, which are related to histones H3, H4, H2A, and H2B, respectively. Each of these TAFs has intrinsic DNA binding activity adjacent to or within the HFD. The DNA binding domains were mapped to evolutionarily conserved and essential regions. Remarkably, HFD-mediated interaction enhanced the DNA binding activity of each of the TAF6-TAF9 and TAF4b-TAF12 pairs and of a histone-like octamer complex composed of the four TAFs. Furthermore, HFD-mediated interaction stimulated sequence-specific binding by TAF6 and TAF9. These results suggest that TAF HFDs merge with other conserved domains for efficient and specific core promoter binding.Transcription of protein-encoding genes in eukaryotes involves the assembly of RNA polymerase II and general transcription factors (GTFs) on the core promoter to form a preinitiation complex (PIC). TFIID is the major DNA-binding GTF. It is composed of the TATA-binding protein (TBP) and 14 TBP-associated factors (TAFs). TAFs regulate transcription at multiple levels. Certain TAFs interact with activators to facilitate PIC formation (2, 18) and transcription reinitiation (1). TAFs also have a role in recognition and binding to core promoter elements. DNase I footprinting revealed direct contact of TAFs with sequences upstream and downstream of the TATA box (11,19,23,26,29,35). TAF1-TAF2 (TAF II 250-TAF II 150) binds the Initiator element (7,33,34), multiple TAFs were cross-linked to the adenovirus major late (AdML) promoter (24), and Drosophila melanogaster TAF6 (dTAF6) and dTAF9 (dTAF II 60-dTAF II 42) were cross-linked to the downstream promoter element (DPE) (5). Some TAFs are TFIID specific, but others are shared by other transcription regulatory complexes (3,4,15,22,25,28).One common feature found in 9 out of the 14 TAFs is the histone fold motif (for a review see reference 13). This motif has been established as an essential protein-protein interaction domain that facilitates assembly of TFIID in a manner analogous to that for histones (17,30). TAF6 and TAF9 are structurally related to histones H4 and H3, respectively (38). TAF12 is similar to H2B, TAF4 contains an H2A-like domain, and both interact with each other via the histone fold domain (HFD) (14,16,30). In vitro Saccharomyces cerevisiae TAF6 (yTAF6)-yTAF9 can assemble with yTAF12-yTAF4 to form a histone octamer-like structure (30).The nucleosome-like interaction of TFIID with DNA (24) and the presence of histone fold TAFs within this complex have led to the proposal that a nucleosome-like octamer within TFIID may be involved in direct DNA binding (17). However, the issue has remained elusive. First, there is no experimental evidence for D...

The RNA polymerase II core promoter — the gateway to transcription

“…Photocrosslinking studies revealed that the DPE is in close proximity to the TFIID subunits TAF6 (TAFII60) and TAF9 (TAFII40), which contain histone fold motifs and are related to histones H4 and H3 [28]. It is thus possible that the TAF6-TAF9 subunits of TFIID interact with the DPE in a manner that is similar to binding of histones H3-H4 to DNA in nucleosomes [29].…”

TAF4/4b·TAF12 Displays a Unique Mode of DNA Binding and Is Required for Core Promoter Function of a Subset of Genes

“…In addition certain TAF subcomplexes have been reported to specifically bind different core promoter elements. The TAF1⅐TAF2 complex binds to the Initiator element (14) and Drosophila TAF6 and TAF9 crosslinked to the downstream promoter element in the context of TFIID (15), and, as a reconstituted complex, these were shown to associate with a downstream promoter element-containing promoter (16).…”

Distinct modes of gene regulation by a cell-specific transcriptional activator

“…Second is that both are sites of known ␤-thalassemia point mutations (16,17,36). Third is that TAF9, in combination with TAF6, is thought to interact with promoters that contain these elements (7,8). As a result, we used gel-shift assays to directly test whether TAF9 can interact with any of these regions.…”

“…Of particular relevance are promoters that contain important sequence elements that lie downstream of the transcription initiation site (1,2,6). Mammalian TAF1, TAF9, TAF6, TAF4b, and TAF12 all contact DNA (7). But more specifically, TAF9 is thought to play a role in transcriptional initiation at promoters that contain an imprecisely characterized sequence called the downstream promoter element (DPE), located at around ϩ30 (defining transcription initiation as ϩ1) (1).…”