Genomes and Genes
transcription factor tfiib
Summary: An RNA POLYMERASE II specific transcription factor. It plays a role in assembly of the pol II transcriptional preinitiation complex and has been implicated as a target of gene-specific transcriptional activators.
- Kosa P, Ghosh G, DeDecker B, Sigler P. The 2.1-A crystal structure of an archaeal preinitiation complex: TATA-box-binding protein/transcription factor (II)B core/TATA-box. Proc Natl Acad Sci U S A. 1997;94:6042-7 pubmed
- Roberts D, Stewart A, Huff J, Cairns B. The RNA polymerase III transcriptome revealed by genome-wide localization and activity-occupancy relationships. Proc Natl Acad Sci U S A. 2003;100:14695-700 pubmed..These studies reveal new aspects of the kinetics, dynamics, and targets of the Pol III system. ..
- Vannini A, Cramer P. Conservation between the RNA polymerase I, II, and III transcription initiation machineries. Mol Cell. 2012;45:439-46 pubmed publisher..This review outlines the similarities and differences between these important molecular machines. ..
- Westover K, Bushnell D, Kornberg R. Structural basis of transcription: separation of RNA from DNA by RNA polymerase II. Science. 2004;303:1014-6 pubmed..This separation of nucleic acid strands is brought about by interaction with a set of proteins loops in a strand/loop network. Formation of the network must occur in the transition from abortive initiation to promoter escape. ..
- Tran K, Gralla J. Control of the timing of promoter escape and RNA catalysis by the transcription factor IIb fingertip. J Biol Chem. 2008;283:15665-71 pubmed publisher..These initiation requirements may assist in RNA quality control by minimizing functional synthesis when RNA polymerase becomes inappropriately associated with the genome without having been recruited there by TFIIB. ..
- Choi W, Yan M, Nusinow D, Gralla J. In vitro transcription and start site selection in Schizosaccharomyces pombe. J Mol Biol. 2002;319:1005-13 pubmed..cerevisiae TFIIB was not accepted. The results enlarge the potential for using fission yeast to study the properties of general transcription factors such as TFIIB in choosing the sites at which transcription initiates. ..
- Elsby L, O Donnell A, Green L, Sharrocks A, Roberts S. Assembly of transcription factor IIB at a promoter in vivo requires contact with RNA polymerase II. EMBO Rep. 2006;7:898-903 pubmedThe general transcription factor TFIIB has a central role in the assembly of the preinitiation complex at the promoter, providing a platform for the entry of RNA polymerase II/TFIIF...
- Kaufmann J, Verrijzer C, Shao J, Smale S. CIF, an essential cofactor for TFIID-dependent initiator function. Genes Dev. 1996;10:873-86 pubmed..Further elucidation of these differences is likely to explain the need for the core promoter heterogeneity found within protein-coding genes. ..
- Geisberg J, Holstege F, Young R, Struhl K. Yeast NC2 associates with the RNA polymerase II preinitiation complex and selectively affects transcription in vivo. Mol Cell Biol. 2001;21:2736-42 pubmed..Thus, NC2 is associated with the Pol II preinitiation complex, and it can play a direct and positive role at certain promoters in vivo. ..
- Deng W, Roberts S. TFIIB and the regulation of transcription by RNA polymerase II. Chromosoma. 2007;116:417-29 pubmed..The general transcription factor TFIIB plays a central role in preinitiation complex assembly, providing a bridge between promoter-bound TFIID ..
- Shandilya J, Wang Y, Roberts S. TFIIB dephosphorylation links transcription inhibition with the p53-dependent DNA damage response. Proc Natl Acad Sci U S A. 2012;109:18797-802 pubmed publisher..Our data reveal a mode of phospho-TFIIB-independent transcriptional regulation that prioritizes the transcription of p53-target genes during cellular stress. ..
- Martinez E. Multi-protein complexes in eukaryotic gene transcription. Plant Mol Biol. 2002;50:925-47 pubmed..Another emerging theme is the multi-functional nature of chromatin-modifying cofactor complexes that appear to couple gene-specific transcription to other cellular processes. ..
- Kimura M, Ishihama A. Tfg3, a subunit of the general transcription factor TFIIF in Schizosaccharomyces pombe, functions under stress conditions. Nucleic Acids Res. 2004;32:6706-15 pubmed..Taken together, we propose that Tfg3 is involved in transcriptional regulation under stress conditions, in particular, at high temperatures. ..
- Albert T, Grote K, Boeing S, Stelzer G, Schepers A, Meisterernst M. Global distribution of negative cofactor 2 subunit-alpha on human promoters. Proc Natl Acad Sci U S A. 2007;104:10000-5 pubmed..Our data establish the genome-wide basis for general and gene-specific functions of NC2 in mammalian cells. ..
- Cabart P, Újvári A, Pal M, Luse D. Transcription factor TFIIF is not required for initiation by RNA polymerase II, but it is essential to stabilize transcription factor TFIIB in early elongation complexes. Proc Natl Acad Sci U S A. 2011;108:15786-91 pubmed publisher..However, if TFIIF is not retained in the PIC, TFIIB can be lost immediately after initiation. TFIIF therefore has an important role in stabilizing TFIIB within the PIC and after transcription initiates. ..
- Ranish J, Yudkovsky N, Hahn S. Intermediates in formation and activity of the RNA polymerase II preinitiation complex: holoenzyme recruitment and a postrecruitment role for the TATA box and TFIIB. Genes Dev. 1999;13:49-63 pubmed..These results demonstate an involvement of TFIIB and the TATA box in one or more steps after recruitment of factors to the promoter. ..
- Sun Z, Hampsey M. Synthetic enhancement of a TFIIB defect by a mutation in SSU72, an essential yeast gene encoding a novel protein that affects transcription start site selection in vivo. Mol Cell Biol. 1996;16:1557-66 pubmed..We discuss the possibility that the potential zinc binding motif of Ssu72 facilitates assembly of the transcription preinitiation complex and that this effect is important for accurate start site selection in vivo. ..
- Imoberdorf R, Topalidou I, Strubin M. A role for gcn5-mediated global histone acetylation in transcriptional regulation. Mol Cell Biol. 2006;26:1610-6 pubmed..These data support a role for global Gcn5 HAT activity in modulating transcription independently of its known coactivator function. ..
- Masters K, Parkhurst K, Daugherty M, Parkhurst L. Native human TATA-binding protein simultaneously binds and bends promoter DNA without a slow isomerization step or TFIIB requirement. J Biol Chem. 2003;278:31685-90 pubmed..Possible sources of these significant differences are discussed. ..
- Wiesler S, Weinzierl R. The linker domain of basal transcription factor TFIIB controls distinct recruitment and transcription stimulation functions. Nucleic Acids Res. 2011;39:464-74 pubmed publisher..The identification of superstimulating TFIIB variants reveals the existence of a previously unknown rate-limiting step acting on the earliest stages of gene expression. ..
- El Kaderi B, Medler S, Raghunayakula S, Ansari A. Gene looping is conferred by activator-dependent interaction of transcription initiation and termination machineries. J Biol Chem. 2009;284:25015-25 pubmed publisher..Instead, activators physically interacted with the general transcription factor TFIIB when the genes were activated and in a looped configuration...
- Littlefield O, Korkhin Y, Sigler P. The structural basis for the oriented assembly of a TBP/TFB/promoter complex. Proc Natl Acad Sci U S A. 1999;96:13668-73 pubmed..immediately upstream of the TATA box called the B recognition element (BRE), so named because eukaryal transcription factor TFIIB and its archaeal orthologue TFB interact with the element in a sequence-specific manner...
- Pappas D, Hampsey M. Functional interaction between Ssu72 and the Rpb2 subunit of RNA polymerase II in Saccharomyces cerevisiae. Mol Cell Biol. 2000;20:8343-51 pubmed..gene encoding a phylogenetically conserved protein of unknown function that interacts with the general transcription factor TFIIB. A recessive ssu72-1 allele was identified as a synthetic enhancer of a TFIIB (sua7-1) defect, resulting ..
- 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. ..
- Hagemeier C, Bannister A, Cook A, Kouzarides T. The activation domain of transcription factor PU.1 binds the retinoblastoma (RB) protein and the transcription factor TFIID in vitro: RB shows sequence similarity to TFIID and TFIIB. Proc Natl Acad Sci U S A. 1993;90:1580-4 pubmed..The potential for RB to influence transcription by using TFIID- and TFIIB-related functions is discussed. ..
- Chen H, Legault P, Glushka J, Omichinski J, Scott R. Structure of a (Cys3His) zinc ribbon, a ubiquitous motif in archaeal and eucaryal transcription. Protein Sci. 2000;9:1743-52 pubmed
- Faitar S, Brodie S, Ponticelli A. Promoter-specific shifts in transcription initiation conferred by yeast TFIIB mutations are determined by the sequence in the immediate vicinity of the start sites. Mol Cell Biol. 2001;21:4427-40 pubmed..We discuss these results in light of possible models for the mechanism of start site utilization by S. cerevisiae RNA polymerase II and the role played by TFIIB. ..
- Magill C, Jackson S, Bell S. Identification of a conserved archaeal RNA polymerase subunit contacted by the basal transcription factor TFB. J Biol Chem. 2001;276:46693-6 pubmed..Intriguingly, homologues of RpoK are found in all three nuclear RNA polymerases (Rpb6) and also in the bacterial RNA polymerase (omega-subunit). ..
- Pal M, Ponticelli A, Luse D. The role of the transcription bubble and TFIIB in promoter clearance by RNA polymerase II. Mol Cell. 2005;19:101-10 pubmed..Our results indicate that bubble collapse defines the RNA polymerase II promoter clearance transition. ..
- Chen H, Hahn S. Mapping the location of TFIIB within the RNA polymerase II transcription preinitiation complex: a model for the structure of the PIC. Cell. 2004;119:169-80 pubmedBiochemical probes positioned on the surface of the general transcription factor TFIIB were used to probe the architecture of the RNA polymerase II (Pol II) transcription preinitiation complex (PIC)...
- Chen B, Hampsey M. Functional interaction between TFIIB and the Rpb2 subunit of RNA polymerase II: implications for the mechanism of transcription initiation. Mol Cell Biol. 2004;24:3983-91 pubmedThe general transcription factor TFIIB is required for accurate initiation, although the mechanism by which RNA polymerase II (RNAP II) identifies initiation sites is not well understood...
- Liu Y, Dong W, Chen L, Zhang P, Qi Y. Characterization of Bcl10 as a potential transcriptional activator that interacts with general transcription factor TFIIB. Biochem Biophys Res Commun. 2004;320:1-6 pubmed..Together, these findings suggest that Bcl10 nuclear expression may modulate gene expression and Bcl10 is a potential transcriptional activator apart from its traditional roles that have been found. ..
- Glossop J, Dafforn T, Roberts S. A conformational change in TFIIB is required for activator-mediated assembly of the preinitiation complex. Nucleic Acids Res. 2004;32:1829-35 pubmed..Strikingly though, an activator fails to recruit the TFIIB mutant to the promoter. Taken together, our results show that a TFIIB conformational change is critical for the formation of activator-dependent transcription complexes. ..
- Fishburn J, Hahn S. Architecture of the yeast RNA polymerase II open complex and regulation of activity by TFIIF. Mol Cell Biol. 2012;32:12-25 pubmed publisher..Together, our results show an unexpected architecture of minimal open complexes and the regulation of activity by TFIIF and the TFIIB core domain. ..
- Sevilimedu A, Shi H, Lis J. TFIIB aptamers inhibit transcription by perturbing PIC formation at distinct stages. Nucleic Acids Res. 2008;36:3118-27 pubmed publisher..report the isolation and characterization of high-affinity RNA aptamers that bind to the yeast general transcription factor TFIIB. These aptamers fall into two classes that interfere with TFIIB's interactions with either TBP or RNA ..
- Tsai F, Sigler P. Structural basis of preinitiation complex assembly on human pol II promoters. EMBO J. 2000;19:25-36 pubmed..Binding of TFIIBc is, therefore, synergistic with TBPc requiring the distortion of the TATA-box. Thus, the newly described TFIIBc-DNA interface is likely to be a key determinant for the unidirectional assembly of a functional PIC. ..
- Fairley J, Evans R, Hawkes N, Roberts S. Core promoter-dependent TFIIB conformation and a role for TFIIB conformation in transcription start site selection. Mol Cell Biol. 2002;22:6697-705 pubmedThe general transcription factor TFIIB plays a central role in the selection of the transcription initiation site. The mechanisms involved are not clear, however...
- Cho E, Buratowski S. Evidence that transcription factor IIB is required for a post-assembly step in transcription initiation. J Biol Chem. 1999;274:25807-13 pubmed..This step may be related to the yeast-specific spacing between TATA elements and start sites since mutations of the corresponding glutamate in mammalian TFIIB do not produce a similar effect. ..
- Liu S, Balasov M, Wang H, Wu L, Chesnokov I, Liu Y. Structural analysis of human Orc6 protein reveals a homology with transcription factor TFIIB. Proc Natl Acad Sci U S A. 2011;108:7373-8 pubmed publisher..This domain has an overall fold similar to the corresponding helical domain of transcription factor TFIIB. Based on these findings, a model of Orc6 binding to DNA is produced...
- Roeder R. The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem Sci. 1996;21:327-35 pubmed
- Dion V, Coulombe B. Interactions of a DNA-bound transcriptional activator with the TBP-TFIIA-TFIIB-promoter quaternary complex. J Biol Chem. 2003;278:11495-501 pubmed
- Henriques T, Ji Z, Tan Wong S, Carmo A, Tian B, Proudfoot N, et al. Transcription termination between polo and snap, two closely spaced tandem genes of D. melanogaster. Transcription. 2012;3:198-212 pubmed..Taken together, our results indicate that polo forms a gene loop and polo transcription termination occurs by an Xrn2 and Pcf11 independent mechanism that requires TFIIB. ..
- Imbalzano A, Zaret K, Kingston R. Transcription factor (TF) IIB and TFIIA can independently increase the affinity of the TATA-binding protein for DNA. J Biol Chem. 1994;269:8280-6 pubmed..We suggest that this property of TFIIA and TFIIB may increase the range of conditions under which high affinity TBP-DNA interactions can occur and may therefore favor the formation of the preinitiation complex. ..
- Hori R, Pyo S, Carey M. Protease footprinting reveals a surface on transcription factor TFIIB that serves as an interface for activators and coactivators. Proc Natl Acad Sci U S A. 1995;92:6047-51 pubmed..One of these interactions is the VP16-mediated binding and recruitment of transcription factor TFIIB. However, TATA box-binding protein (TBP)-associated factors (TAFs), or coactivators, are required for ..
- Wang Y, Fairley J, Roberts S. Phosphorylation of TFIIB links transcription initiation and termination. Curr Biol. 2010;20:548-53 pubmed publisherThe general transcription factor TFIIB plays a central role in preinitiation complex (PIC) assembly and the recruitment of RNA polymerase II (RNA pol II) to the promoter...
- Veschambre P, Roisin A, Jalinot P. Biochemical and functional interaction of the human immunodeficiency virus type 1 Tat transactivator with the general transcription factor TFIIB. J Gen Virol. 1997;78 ( Pt 9):2235-45 pubmed..From these data we propose a model in which interaction between Tat and both general transcription factors TBP and TFIIB maintains the transcriptional initiation complex in an active configuration. ..
- Bell S, Jackson S. The role of transcription factor B in transcription initiation and promoter clearance in the archaeon Sulfolobus acidocaldarius. J Biol Chem. 2000;275:12934-40 pubmed..Finally, we identify the promoter sequences responsive to this mutation and demonstrate that the effect of the mutation is to block a late stage in transcription initiation, following formation of the promoter open complex...
- Takagi Y, Calero G, Komori H, Brown J, Ehrensberger A, Hudmon A, et al. Head module control of mediator interactions. Mol Cell. 2006;23:355-64 pubmed..The head module evidently controls Mediator-RNA polymerase II and Mediator-promoter interactions. ..
- Evans R, Fairley J, Roberts S. Activator-mediated disruption of sequence-specific DNA contacts by the general transcription factor TFIIB. Genes Dev. 2001;15:2945-9 pubmedThe transcription factor TFIIB plays a central role in preinitiation complex assembly, providing a bridge between promoter-bound TFIID and RNA Polymerase II...
- Berroteran R, Ware D, Hampsey M. The sua8 suppressors of Saccharomyces cerevisiae encode replacements of conserved residues within the largest subunit of RNA polymerase II and affect transcription start site selection similarly to sua7 (TFIIB) mutations. Mol Cell Biol. 1994;14:226-37 pubmed..cerevisiae and suggest that this function might be conferred by interaction between these two proteins. ..
- Kuras L, Rouillon A, Lee T, Barbey R, Tyers M, Thomas D. Dual regulation of the met4 transcription factor by ubiquitin-dependent degradation and inhibition of promoter recruitment. Mol Cell. 2002;10:69-80 pubmed