TATA element recognition by the TATA box-binding protein has been conserved throughout evolution

Patikoglou, Georgia A.; Kim, Joseph L.; Sun, Liping; Yang, Sanghwa; Kodadek, Thomas; Burley, S.K.

doi:10.1101/gad.13.24.3217

Cited by 277 publications

(354 citation statements)

References 55 publications

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“…TBPs have a very specific site of interaction with DNA, which usually includes guanine residues [31]. In yeast, the major TBP, called SpT15, binds to the GNNATATATA motif [30], ahead of the starting codon in genes.…”

Section: Homologue Chromosome Recognition In Meiosismentioning

confidence: 99%

The distribution of alternating AT sequences in eukaryotic genomes suggests a role in homologous chromosome recognition in meiosis

Subirana

Messeguer

2011

Journal of Theoretical Biology

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There are general features of chromosome dynamics, such as homologue recognition in early meiosis, which are expected to involve related sequence motifs in non-coding DNA, with a similar distribution in different species. A search for such motifs is presented here. It has been carried out with the CONREPP program. It has been found that short alternating AT sequences (10-20 bases) have a similar distribution in most eukaryotic organisms, with some exceptions related to unique meiotic features. All other microsatellite and repeat sequences vary significantly in different organisms. It is concluded that the unique structural features and uniform distribution of alternating AT sequences indicate that they may facilitate homologous chromosome pairing in the early preleptotene stage of meiosis. They may also play a role in the compaction of DNA in mitotic chromosomes.

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Section: Homologue Chromosome Recognition In Meiosismentioning

confidence: 99%

The distribution of alternating AT sequences in eukaryotic genomes suggests a role in homologous chromosome recognition in meiosis

Subirana

Messeguer

2011

Journal of Theoretical Biology

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“…1 and references therein and Refs. [2][3][4][5][6][7][8][9][10][11]. The extent of the DNA TATA bending is TATA sequence-dependent in solution (8,9,12,13).…”

mentioning

confidence: 94%

“…A limited answer has emerged from crystallographic studies on the C-terminal domains of yTBP and hTBP and the (analogous) full-length aTBP, bound to DNA TATA : the structures of these three TBP-DNA complexes are essentially identical in the crystalline form (2,17,18) and are TATA sequence-independent at least for yTBP (6). Beyond these results, however, comparisons of the behavior of yTBP, hTBP, and aTBP with DNA TATA and the structures of the resulting binary complexes must be inferred from unrelated experiments conducted in different laboratories using any one of these three proteins, either as the full-length or truncated C-terminal form.…”

mentioning

confidence: 99%

Native Human TATA-binding Protein Simultaneously Binds and Bends Promoter DNA without a Slow Isomerization Step or TFIIB Requirement

Masters

Parkhurst

Daugherty

et al. 2003

Journal of Biological Chemistry

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The association of TATA-binding protein (TBP) with promoter DNA is central to the initiation and regulation of eukaryotic protein synthesis. Our laboratory has previously conducted detailed investigations of this interaction using yeast TBP and seven consensus and variant TATA sequences. We have now investigated this key interaction using human TBP and the TATA sequence from the adenovirus major late promoter (AdMLP). Recombinant native human protein was used together with fluorescently labeled DNA, allowing real time data acquisition in solution. We find that the wild-type hTBP-DNA AdMLP reaction is characterized by high affinity (K d ‫؍‬ 5 nM), simultaneous binding and DNA bending, and rapid formation of a stable human TBP-DNA complex having DNA bent ϳ100°. These data allow, for the first time, a direct comparison of the reactions of the full-length, native human and yeast TBPs with a consensus promoter, studied under identical conditions. The general reaction characteristics are similar for the human and yeast proteins, although the details differ and the hTBP wt -induced bend is more severe. This directly measured hTBP wt -DNA AdMLP interaction differs fundamentally from a recently published hTBP wt -DNA AdMLP model characterized by low affinity ( M) binding and an unstable complex requiring either a 30-min isomerization or TFIIB to achieve DNA bending. Possible sources of these significant differences are discussed.The recognition and binding of promoter TATA sequences (DNA TATA ) 1 by the TATA-binding protein (TBP) is central to the initiation and regulation of gene transcription in eukaryotes. The importance of the TBP-DNA TATA interaction has prompted extensive biochemical and biophysical investigations, which have revealed complex binding mechanisms and dramatic TBP-induced helical distortion, including DNA TATA bending and unwinding (see Ref. 1 and references therein and Refs. 2-11). The extent of the DNA TATA bending is TATA sequence-dependent in solution (8,9,12,13). Because these collective results have been obtained using different TBPs, full-length and truncated proteins, and diverse experimental conditions, key issues relating to the behavior and structure of TBP-promoter complexes remain unresolved.The 180-residue C-terminal DNA binding domains (CTD) of the TBPs from yeast (yTBP), human (hTBP), and Arabidopsis thaliana (aTBP) are highly conserved, with greater than 80% homology and with generally conservative substitutions in the remainder. The pseudo-symmetric TBP CTD contacts the duplex along the distorted minor groove via interactions that are largely non-polar and hydrophobic. The amino acid residues involved in these DNA contacts are nearly 100% conserved, with only a single variation in which Arg-204 in hTBP changes to Lys-110 in yTBP and Lys-68 in aTBP (2). The N-terminal domain is, in contrast, heterogenous between the yeast (60 amino acids (14)) and human (159 amino acids (15)) proteins and severely truncated in the A. thaliana protein (18 amino acids (16)).How these similarities and di...

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“…The presence of a C at position 5 of the TATA box is highly unusual and has not been observed in any of the 900 characterized promoters described in the eukaryotic promoter database (EPD). In addition, it has been shown experimentally that the presence of a C at this position will disrupt the interaction with the TATA binding protein (TBP; Patikoglou et al 1999;Praz et al 2002). The P Transposase promoter also lacks Initiator and DPE elements.…”

Section: Phosphorylation Of H3 Might Require Binding Of Tbp At the Comentioning

confidence: 99%

Phosphorylation of histone H3 during transcriptional activation depends on promoter structure

Labrador¹,

Corcés²

2003

Genes Dev.

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Covalent modifications of histone N-terminal tails are required for the proper assembly and activation of the general transcription factors at promoters. Here, we analyze histone acetylation and phosphorylation in Drosophila transgenes activated by the yeast Gal4 transcriptional activator in the context of different promoters. We show that, independent of the promoter, transcription does not correlate with acetylation of either H3-Lys 14 or H4-Lys 8. Histone H3 associated with the DNA of Gal4-induced transcribing transgenes driven by the Drosophila Hsp70 promoter is hyperphosphorylated at Ser 10 during transcription. Surprisingly, histone H3 at Gal4-induced transgenes driven by the P element Transposase promoter is not hyperphosphorylated. The data suggest that transcription occurs without acetylated H4 and H3 in both transgenes in Drosophila polytene chromosomes. Instead, phosphorylation of H3 is linked to transcription and can be modulated by the structure of the promoter. Received July 8, 2002; revised version accepted October 31, 2002. Posttranslational covalent modifications of N-terminal tails of the core histones at the nucleosome play an important role in determining chromatin structure, which is an essential component of the control of nuclear biology (Jenuwein and Allis 2001). The expression of a large number of genes from organisms across the phylogenetic scale correlates with histone modifications such as acetylation, methylation, phosphorylation, and ubiquitination in the nucleosomes surrounding the promoter of the gene (Roth et al. 2001;Berger 2002;Fry and Peterson 2002;Sun and Allis 2002). Acetylation of histones H3 and H4 N-terminal tails has been broadly associated with activation of transcription. Histone acetyl-transferases (HATs) are found in a variety of coactivators and transcription factor complexes, whereas histone deacetylases (HDACs) are present in protein complexes with a repressive function (Roth et al. 2001). H3 methylation at Lys 9 has the opposite effect and therefore is found in regions where transcription is repressed by chromatin structure (Rea et al. 2000;Bannister et al. 2001). Phosphorylation of H3 at Ser 10 has also been correlated with activation of transcription in yeast, mammals, and Drosophila (Cheung et al. 2000;Lo et al. 2000;Nowak and Corces 2000;Lo et al. 2001;Thomson et al. 2001;Li et al. 2002;Strelkov and Davie 2002).Two nonexclusive models have been postulated to explain the role of histone N-terminal tail modification in transcription. The first one suggests that histone modifications have an effect on the relative charge of the histone tails, rendering a more open or closed chromatin state that determines the accessibility of transcription factors to the core promoter. The second model, termed the histone code hypothesis, predicts that a combination of covalent modifications of histone tails functions as a target for the specific binding of effector proteins (Turner 2000;Jenuwein and Allis 2001). Binding of these proteins will ultimately determine the transc...

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TATA element recognition by the TATA box-binding protein has been conserved throughout evolution

Cited by 277 publications

References 55 publications

The distribution of alternating AT sequences in eukaryotic genomes suggests a role in homologous chromosome recognition in meiosis

The distribution of alternating AT sequences in eukaryotic genomes suggests a role in homologous chromosome recognition in meiosis

Native Human TATA-binding Protein Simultaneously Binds and Bends Promoter DNA without a Slow Isomerization Step or TFIIB Requirement

Phosphorylation of histone H3 during transcriptional activation depends on promoter structure

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