Genomes and Genes
tata box binding protein
Summary: A general transcription factor that plays a major role in the activation of eukaryotic genes transcribed by RNA POLYMERASES. It binds specifically to the TATA BOX promoter element, which lies close to the position of transcription initiation in RNA transcribed by RNA POLYMERASE II. Although considered a principal component of TRANSCRIPTION FACTOR TFIID it also takes part in general transcription factor complexes involved in RNA POLYMERASE I and RNA POLYMERASE III transcription.
- Maltecca F, Filla A, Castaldo I, Coppola G, Fragassi N, Carella M, et al. Intergenerational instability and marked anticipation in SCA-17. Neurology. 2003;61:1441-3 pubmed..Molecular analysis demonstrated an expanded CAG/CAA repeat in the TBP gene (SCA-17). The repeat size was 66 triplets in the child and 53 in all the other patients. ..
- Gumbs O, Campbell A, Weil P. High-affinity DNA binding by a Mot1p-TBP complex: implications for TAF-independent transcription. EMBO J. 2003;22:3131-41 pubmed..We propose that this altered TBP-DNA recognition is integral to Mot1p's ability to regulate transcription, and further postulate that the Mot1p-TBP complex delivers TBP to TAF-independent mRNA encoding genes. ..
- Das A, Zhang Q, Palenchar J, Chatterjee B, Cross G, Bellofatto V. Trypanosomal TBP functions with the multisubunit transcription factor tSNAP to direct spliced-leader RNA gene expression. Mol Cell Biol. 2005;25:7314-22 pubmed..These findings provide the first view of the architecture of a transcriptional complex that assembles at an RNA polymerase II-dependent gene promoter in a highly divergent eukaryote. ..
- Schimanski B, Nguyen T, GUNZL A. Characterization of a multisubunit transcription factor complex essential for spliced-leader RNA gene transcription in Trypanosoma brucei. Mol Cell Biol. 2005;25:7303-13 pubmed..As we demonstrate, the TRF4/SNAP(c)/TFIIA complex binds specifically to the SL RNA gene promoter upstream sequence element and is absolutely essential for SL RNA gene transcription in vitro. ..
- Raha T, Cheng S, Green M. HIV-1 Tat stimulates transcription complex assembly through recruitment of TBP in the absence of TAFs. PLoS Biol. 2005;3:e44 pubmed..Thus, in mammalian cells transcription of protein-coding genes involves alternative TCs that differ by the presence or absence of TAFs. ..
- Huisinga K, Pugh B. A TATA binding protein regulatory network that governs transcription complex assembly. Genome Biol. 2007;8:R46 pubmed..The findings further demonstrate the interconnections of TBP regulation on a genome-wide scale. ..
- Fan X, Shi H, Adelman K, Lis J. Probing TBP interactions in transcription initiation and reinitiation with RNA aptamers that act in distinct modes. Proc Natl Acad Sci U S A. 2004;101:6934-9 pubmed..In crude cell extracts, the aptamers inhibit transcription in ways that reveal the dynamic nature of TBP interactions during initiation and reinitiation. ..
- van Roon Mom W, Reid S, Jones A, MacDonald M, Faull R, Snell R. Insoluble TATA-binding protein accumulation in Huntington's disease cortex. Brain Res Mol Brain Res. 2002;109:1-10 pubmed..At least a proportion of this accumulated TBP exists as insoluble protein. This suggests that TBP may play a role in the disease process. ..
- Darst R, Dasgupta A, Zhu C, Hsu J, Vroom A, Muldrow T, et al. Mot1 regulates the DNA binding activity of free TATA-binding protein in an ATP-dependent manner. J Biol Chem. 2003;278:13216-26 pubmed..A model for Mot1 action is proposed in which ATP hydrolysis causes the Mot1 N terminus to displace the TATA box, leading to ejection of Mot1 and TBP from DNA. ..
- Isogai Y, Keles S, Prestel M, Hochheimer A, Tjian R. Transcription of histone gene cluster by differential core-promoter factors. Genes Dev. 2007;21:2936-49 pubmed..Our studies establish that TRF2 promoter recognition complexes play a significantly more central role in governing metazoan transcription than previously appreciated. ..
- Strahs D, Barash D, Qian X, Schlick T. Sequence-dependent solution structure and motions of 13 TATA/TBP (TATA-box binding protein) complexes. Biopolymers. 2003;69:216-43 pubmedThe TATA element is a well-known example of a DNA promoter sequence recognized by the TATA box binding protein (TBP) through its intrinsic motion and deformability...
- Jacobi U, Akkers R, Pierson E, Weeks D, Dagle J, Veenstra G. TBP paralogs accommodate metazoan- and vertebrate-specific developmental gene regulation. EMBO J. 2007;26:3900-9 pubmed publisher..A requirement for TBP2 is linked to vertebrate-specific embryonic genes and ventral-specific expression. Therefore TBP paralogs are essential for the gene-regulatory repertoire that is directly linked to early embryogenesis...
- Rolfs A, Koeppen A, Bauer I, Bauer P, Buhlmann S, Topka H, et al. Clinical features and neuropathology of autosomal dominant spinocerebellar ataxia (SCA17). Ann Neurol. 2003;54:367-75 pubmed..Based on clinical and genetic data, we conclude that SCA17 is rare among white SCA patients. SCA17 should be considered in sporadic and familial cases of ataxia with accompanying psychiatric symptoms and dementia. ..
- Hieb A, Halsey W, Betterton M, Perkins T, Kugel J, Goodrich J. TFIIA changes the conformation of the DNA in TBP/TATA complexes and increases their kinetic stability. J Mol Biol. 2007;372:619-32 pubmed..Furthermore, we present a refined model for the effect that TFIIA has on DNA conformation that takes into account potential changes in bend angle as well as twist angle. ..
- Kieffer Kwon P, Martianov I, Davidson I. Cell-specific nucleolar localization of TBP-related factor 2. Mol Biol Cell. 2004;15:4356-68 pubmed..Although partially contradictory results have been reported, our data are consistent with a model where only small proportion of the cellular TBP remains associated with specific promoter loci during mitosis. ..
- Warfield L, Ranish J, Hahn S. Positive and negative functions of the SAGA complex mediated through interaction of Spt8 with TBP and the N-terminal domain of TFIIA. Genes Dev. 2004;18:1022-34 pubmed..Our results suggest a mechanism for the previously observed positive and negative effects of Spt8 on transcription observed in vivo. ..
- Pereira L, Klejman M, Ruhlmann C, Kavelaars F, Oulad Abdelghani M, Timmers H, et al. Molecular architecture of the basal transcription factor B-TFIID. J Biol Chem. 2004;279:21802-7 pubmed..Comparison of the native B-TFIID with its recombinant form shows that both share a similar domain organization. Collectively, these data provide the first structural model of the B-TFIID complex and map its key functional domains. ..
- van Roon Mom W, Reid S, Faull R, Snell R. TATA-binding protein in neurodegenerative disease. Neuroscience. 2005;133:863-72 pubmed..The role of TBP in other polyglutamine disorders will be addressed as well as its possible role in other neurodegenerative diseases. ..
- Bush S, Richard P, Manley J. Variations in intracellular levels of TATA binding protein can affect specific genes by different mechanisms. Mol Cell Biol. 2008;28:83-92 pubmed
- Bauer P, Laccone F, Rolfs A, Wullner U, Bosch S, Peters H, et al. Trinucleotide repeat expansion in SCA17/TBP in white patients with Huntington's disease-like phenotype. J Med Genet. 2004;41:230-2 pubmed
- Schaffar G, Breuer P, Boteva R, Behrends C, Tzvetkov N, Strippel N, et al. Cellular toxicity of polyglutamine expansion proteins: mechanism of transcription factor deactivation. Mol Cell. 2004;15:95-105 pubmed..These results outline a molecular mechanism of cellular toxicity in polyQ disease and can explain the beneficial effects of molecular chaperones. ..
- Kou H, Irvin J, Huisinga K, Mitra M, Pugh B. Structural and functional analysis of mutations along the crystallographic dimer interface of the yeast TATA binding protein. Mol Cell Biol. 2003;23:3186-201 pubmed..These phenotypes cannot be accounted for by defective interactions with other known TBP inhibitors and likely reflect defects in TBP dimerization. ..
- Martianov I, Viville S, Davidson I. RNA polymerase II transcription in murine cells lacking the TATA binding protein. Science. 2002;298:1036-9 pubmed..Our results show a differential dependency of the RNA polymerases on TBP and provide evidence for TBP-independent pol II transcriptional mechanisms that allow reinitiation and maintenance of gene transcription in vivo. ..
- Davidson I. The genetics of TBP and TBP-related factors. Trends Biochem Sci. 2003;28:391-8 pubmed
- Faiger H, Ivanchenko M, Cohen I, Haran T. TBP flanking sequences: asymmetry of binding, long-range effects and consensus sequences. Nucleic Acids Res. 2006;34:104-19 pubmed..We propose that the plasticity of (T-A)n sequences increases the number of conformationally distinct TATA boxes without the need to extent the TBP contact region beyond the eight-base-pair long TATA box. ..
- Gilfillan S, Stelzer G, Piaia E, Hofmann M, Meisterernst M. Efficient binding of NC2.TATA-binding protein to DNA in the absence of TATA. J Biol Chem. 2005;280:6222-30 pubmed..DNA complexes. Our data suggest that NC2 controls TBP binding and maintenance on DNA that is largely independent of a canonical TATA sequence. ..
- Jallow Z, Jacobi U, Weeks D, Dawid I, Veenstra G. Specialized and redundant roles of TBP and a vertebrate-specific TBP paralog in embryonic gene regulation in Xenopus. Proc Natl Acad Sci U S A. 2004;101:13525-30 pubmed..TBP2 may be a TBP replacement factor in oocytes, whereas in embryos both TBP and TBP2 are required even though they exhibit partial redundancy and gene selectivity. ..
- Biswas D, Imbalzano A, Eriksson P, Yu Y, Stillman D. Role for Nhp6, Gcn5, and the Swi/Snf complex in stimulating formation of the TATA-binding protein-TFIIA-DNA complex. Mol Cell Biol. 2004;24:8312-21 pubmed..Consistent with the idea that Nhp6, Gcn5, and Swi/Snf have overlapping functions in vivo, nhp6a nhp6b gcn5 mutants had a severe growth defect, and mutations in both nhp6a nhp6b swi2 and gcn5 swi2 strains were lethal. ..
- Bergqvist S, Williams M, O Brien R, Ladbury J. Halophilic adaptation of protein-DNA interactions. Biochem Soc Trans. 2003;31:677-80 pubmed..Since the halophilic nature of this protein can be attributed to only three mutations, this reveals that the important phenotype of halophilicity could be rapidly acquired in evolutionary time. ..
- Buratowski R, Downs J, Buratowski S. Interdependent interactions between TFIIB, TATA binding protein, and DNA. Mol Cell Biol. 2002;22:8735-43 pubmed..The TBPs with increased affinity could not suppress TFIIB(G204D), leading us to propose a two-step model for the interaction between TFIIB and the TBP-DNA complex. ..
- Chitikila C, Huisinga K, Irvin J, Basehoar A, Pugh B. Interplay of TBP inhibitors in global transcriptional control. Mol Cell. 2002;10:871-82 pubmed..These findings reveal that transcriptional output is limited in part by a collaboration of different combinations of TBP inhibitory mechanisms. ..
- Mousson F, Kolkman A, Pijnappel W, Timmers H, Heck A. Quantitative proteomics reveals regulation of dynamic components within TATA-binding protein (TBP) transcription complexes. Mol Cell Proteomics. 2008;7:845-52 pubmed..Cell cycle synchronization showed that BTAF1 exchange was regulated during mitosis. The combination of the two affinity purification protocols allows a quantitative approach to identify transient components in any protein complex. ..
- Dasgupta A, Juedes S, Sprouse R, Auble D. Mot1-mediated control of transcription complex assembly and activity. EMBO J. 2005;24:1717-29 pubmed..We suggest that at activated promoters, Mot1 disassembles transcriptionally inactive TBP, thereby facilitating the formation of a TBP complex that supports functional PIC assembly. ..
- Waxman S, Wurmbach E. De-regulation of common housekeeping genes in hepatocellular carcinoma. BMC Genomics. 2007;8:243 pubmed..This study assessed eight stages of hepatitis C virus (HCV) induced hepatocellular carcinoma (HCC) to search for appropriate genes for normalization...
- Cang Y, Prelich G. Direct stimulation of transcription by negative cofactor 2 (NC2) through TATA-binding protein (TBP). Proc Natl Acad Sci U S A. 2002;99:12727-32 pubmed..On the basis of these results, we propose a model to explain how NC2 can mediate both repression and activation through the same surface of TBP. ..
- Govind C, Yoon S, Qiu H, Govind S, Hinnebusch A. Simultaneous recruitment of coactivators by Gcn4p stimulates multiple steps of transcription in vivo. Mol Cell Biol. 2005;25:5626-38 pubmed..Our findings reveal a program of coactivator recruitment and PIC assembly that distinguishes Gcn4p from other yeast activators studied thus far. ..
- Fang X, Han H, Stamatoyannopoulos G, Li Q. Developmentally specific role of the CCAAT box in regulation of human gamma-globin gene expression. J Biol Chem. 2004;279:5444-9 pubmed..Our data also suggest that it is unlikely that transcriptional stimulation by the CCAAT box is exerted through direct protein-protein interaction between NF-Y and TBP. ..
- Toyoshima Y, Yamada M, Onodera O, Shimohata M, Inenaga C, Fujita N, et al. SCA17 homozygote showing Huntington's disease-like phenotype. Ann Neurol. 2004;55:281-6 pubmed..Neuronal loss was relatively restricted and most prominent in the Purkinje cell layer and striatum; however, intranuclear neuronal polyglutamine accumulation was widespread, with a high frequency in the cerebral cortex and striatum. ..
- Venters B, Pugh B. A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome. Genome Res. 2009;19:360-71 pubmed publisher..We find PIC assembly, which includes Pol II recruitment, to be a significant rate-limiting step during transcription, but that additional gene-specific rate-limiting steps associated with Pol II occur after recruitment. ..
- van Werven F, van Bakel H, van Teeffelen H, Altelaar A, Koerkamp M, Heck A, et al. Cooperative action of NC2 and Mot1p to regulate TATA-binding protein function across the genome. Genes Dev. 2008;22:2359-69 pubmed publisher..Based on these results, we propose that NC2 and Mot1p cooperate to dynamically restrict TBP activity on transcribed promoters. ..
- Geisberg J, Moqtaderi Z, Kuras L, Struhl K. Mot1 associates with transcriptionally active promoters and inhibits association of NC2 in Saccharomyces cerevisiae. Mol Cell Biol. 2002;22:8122-34 pubmed..We speculate that Mot1 does not form transcriptionally active TBP complexes but rather regulates transcription in vivo by modulating the activity of free TBP and/or by affecting promoter DNA structure. ..
- Zühlke C, Gehlken U, Hellenbroich Y, Schwinger E, Burk K. Phenotypical variability of expanded alleles in the TATA-binding protein gene. Reduced penetrance in SCA17?. J Neurol. 2003;250:161-3 pubmed..Apparently, the expanded allele does not cosegregate with the disease phenotype since the mother and two of the siblings do not show any clinical abnormality. This appears to be the first description of non-penetrance in SCA17. ..
- Bushnell D, Westover K, Davis R, Kornberg R. Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms. Science. 2004;303:983-8 pubmed..The trajectory of promoter DNA determined by the C-terminal domain of TFIIB traverses sites of interaction with TFIIE, TFIIF, and TFIIH, serving to define their roles in the transcription initiation process. ..
- Geisberg J, Struhl K. Cellular stress alters the transcriptional properties of promoter-bound Mot1-TBP complexes. Mol Cell. 2004;14:479-89 pubmed..This suggests that functional preinitiation complexes can contain Mot1 instead of TFIIA in vivo. Thus, Mot1-TBP complexes can exist in active and inactive forms that are regulated by environmental stress. ..
- Shi H, Fan X, Sevilimedu A, Lis J. RNA aptamers directed to discrete functional sites on a single protein structural domain. Proc Natl Acad Sci U S A. 2007;104:3742-6 pubmed..These results should spur innovative approaches to modulating other highly connected regulatory proteins. ..
- Eriksson P, Biswas D, Yu Y, Stewart J, Stillman D. TATA-binding protein mutants that are lethal in the absence of the Nhp6 high-mobility-group protein. Mol Cell Biol. 2004;24:6419-29 pubmed..These results challenge the widely held belief that 6-AU sensitivity results from a defect in transcriptional elongation. ..
- Kumar R, Volk D, Li J, Lee J, Gorenstein D, Thompson E. TATA box binding protein induces structure in the recombinant glucocorticoid receptor AF1 domain. Proc Natl Acad Sci U S A. 2004;101:16425-30 pubmed..factors, including a critical component of the general transcription machinery proteins, the TATA box binding protein (TBP). We tested whether this interaction can lead to acquisition of structure in the GR AF1...
- Wu S, Zhou T, Chiang C. Human mediator enhances activator-facilitated recruitment of RNA polymerase II and promoter recognition by TATA-binding protein (TBP) independently of TBP-associated factors. Mol Cell Biol. 2003;23:6229-42 pubmed..Our data provides biochemical evidence that Mediator functions by facilitating activator-mediated recruitment of pol II and also promoter recognition by TBP, both of which can occur in the absence of TBP-associated factors in TFIID. ..
- Hinkley C, Hirsch H, Gu L, LaMere B, Henry R. The small nuclear RNA-activating protein 190 Myb DNA binding domain stimulates TATA box-binding protein-TATA box recognition. J Biol Chem. 2003;278:18649-57 pubmed..Thus, interactions between the DNA binding domains of SNAP190 and TBP at juxtaposed promoter elements define the assembly of a RNA polymerase III-specific preinitiation complex. ..
- Schmidt E, Davies C. The origins of polypeptide domains. Bioessays. 2007;29:262-70 pubmed..This review discusses these processes and how each might participate in the evolutionary emergence of novel polypeptide domains. ..
- Prigge J, Schmidt E. Interaction of protein inhibitor of activated STAT (PIAS) proteins with the TATA-binding protein, TBP. J Biol Chem. 2006;281:12260-9 pubmed
- Palenchar J, Liu W, Palenchar P, Bellofatto V. A divergent transcription factor TFIIB in trypanosomes is required for RNA polymerase II-dependent spliced leader RNA transcription and cell viability. Eukaryot Cell. 2006;5:293-300 pubmed..The information gleaned from TbTFIIB studies furthers our understanding of SL RNA gene transcription and the elusive overall transcriptional processes in trypanosomes. ..