Genomes and Genes
tfii transcription factors
Summary: The so-called general transcription factors that bind to RNA POLYMERASE II and that are required to initiate transcription. They include TFIIA; TFIIB; TFIID; TFIIE; TFIIF; TFIIH; TFII-I; and TFIIJ. In vivo they apparently bind in an ordered multi-step process and/or may form a large preinitiation complex called RNA polymerase II holoenzyme.
- Di Lello P, Miller Jenkins L, Mas C, Langlois C, Malitskaya E, Fradet Turcotte A, et al. p53 and TFIIEalpha share a common binding site on the Tfb1/p62 subunit of TFIIH. Proc Natl Acad Sci U S A. 2008;105:106-11 pubmed..These results point to an important interplay between the general transcription factor TFIIEalpha and the tumor suppressor protein p53 in regulating transcriptional activation that may be modulated by the phosphorylation status of p53. ..
- Roy A. Signal-induced functions of the transcription factor TFII-I. Biochim Biophys Acta. 2007;1769:613-21 pubmed..Here we discuss how a multitude of signaling inputs target TFII-I isoforms, which may exert their functions in distinct phases of the cell cycle and play a key role in the coordinated regulation of cellular proliferation. ..
- Chang W, Kornberg R. Electron crystal structure of the transcription factor and DNA repair complex, core TFIIH. Cell. 2000;102:609-13 pubmed..The structure is based on a ring of three subunits, Tfb1, Tfb2, and Tfb3, to which are appended several functional moieties: Rad3, bridged to Tfb1 by SsI1; SsI2, known to interact with Tfb2; and Kin28, known to interact with Tfb3. ..
- Chen H, Warfield L, Hahn S. The positions of TFIIF and TFIIE in the RNA polymerase II transcription preinitiation complex. Nat Struct Mol Biol. 2007;14:696-703 pubmed..Together with previous biochemical and structural studies, these findings illuminate the structural organization of the PIC and the network of protein-protein interactions involved in transcription start site selection. ..
- Kobor M, Simon L, Omichinski J, Zhong G, Archambault J, Greenblatt J. A motif shared by TFIIF and TFIIB mediates their interaction with the RNA polymerase II carboxy-terminal domain phosphatase Fcp1p in Saccharomyces cerevisiae. Mol Cell Biol. 2000;20:7438-49 pubmed..These results suggest strongly that this KEFGK motif in RAP74 mediates its interaction with Fcp1p in vivo. ..
- Chen D, Riedl T, Washbrook E, Pace P, Coombes R, Egly J, et al. Activation of estrogen receptor alpha by S118 phosphorylation involves a ligand-dependent interaction with TFIIH and participation of CDK7. Mol Cell. 2000;6:127-37 pubmed..These findings are suggestive of a novel mechanism by which nuclear receptor activity can be regulated by ligand-dependent recruitment of modifying activities, such as kinases. ..
- Rani P, Ranish J, Hahn S. RNA polymerase II (Pol II)-TFIIF and Pol II-mediator complexes: the major stable Pol II complexes and their activity in transcription initiation and reinitiation. Mol Cell Biol. 2004;24:1709-20 pubmed..These results suggest that both the Pol II-Med and Pol II-TFIIF complexes can be recruited for transcription initiation but that only the Pol II-TFIIF complex is competent for transcription reinitiation. ..
- Selleck W, Howley R, Fang Q, Podolny V, Fried M, Buratowski S, et al. A histone fold TAF octamer within the yeast TFIID transcriptional coactivator. Nat Struct Biol. 2001;8:695-700 pubmed..Our results indicate that the TAF octamer is similar both in stoichiometry and histone fold interactions to the histone octamer component of chromatin. ..
- Morris C, Mervis C, Hobart H, Gregg R, Bertrand J, Ensing G, et al. GTF2I hemizygosity implicated in mental retardation in Williams syndrome: genotype-phenotype analysis of five families with deletions in the Williams syndrome region. Am J Med Genet A. 2003;123A:45-59 pubmed..Comparison of these five families with reports of other individuals with partial deletions of the WS region most strongly implicates GTF2I in the mental retardation of WS. ..
- Akashi S, Nagakura S, Yamamoto S, Okuda M, Ohkuma Y, Nishimura Y. Structural characterization of human general transcription factor TFIIF in solution. Protein Sci. 2008;17:389-400 pubmed publisher..This is consistent with the previous photo-cross-linking observation that TFIIF and TFIIE flank DNA separately on both sides of the Pol II central cleft in the yeast PIC. ..
- Okuda M, Tanaka A, Arai Y, Satoh M, Okamura H, Nagadoi A, et al. A novel zinc finger structure in the large subunit of human general transcription factor TFIIE. J Biol Chem. 2004;279:51395-403 pubmed
- Di Lello P, Jenkins L, Jones T, Nguyen B, Hara T, Yamaguchi H, et al. Structure of the Tfb1/p53 complex: Insights into the interaction between the p62/Tfb1 subunit of TFIIH and the activation domain of p53. Mol Cell. 2006;22:731-40 pubmed..These results indicate that a phosphorylation cascade involving Ser46 and Thr55 of p53 could play an important role in the regulation of select p53 target genes. ..
- Yamamoto S, Watanabe Y, van der Spek P, Watanabe T, Fujimoto H, Hanaoka F, et al. Studies of nematode TFIIE function reveal a link between Ser-5 phosphorylation of RNA polymerase II and the transition from transcription initiation to elongation. Mol Cell Biol. 2001;21:1-15 pubmed..These observations provide evidence of TFIIE involvement in the transition and suggest that Ser-5 phosphorylation is essential for Pol II to be in the processive elongation form. ..
- Matangkasombut O, Buratowski R, Swilling N, Buratowski S. Bromodomain factor 1 corresponds to a missing piece of yeast TFIID. Genes Dev. 2000;14:951-62 pubmed..The structural and functional similarities suggest that Bdf1 corresponds to the carboxy-terminal region of higher eukaryotic TAF(II)250 and that the interaction between TFIID and Bdf1 is important for proper gene expression. ..
- Chen B, Mandal S, Hampsey M. High-resolution protein-DNA contacts for the yeast RNA polymerase II general transcription machinery. Biochemistry. 2004;43:12741-9 pubmed..We discuss the implications of these results for the mechanism of preinitiation complex assembly and promoter melting. ..
- Tirode F, Busso D, Coin F, Egly J. Reconstitution of the transcription factor TFIIH: assignment of functions for the three enzymatic subunits, XPB, XPD, and cdk7. Mol Cell. 1999;3:87-95 pubmed..In addition, we also show that cdk7 may phosphorylate the carboxy-terminal domain (CTD) of RNA pol II in the absence of promoter opening. ..
- Gervais V, Lamour V, Jawhari A, Frindel F, Wasielewski E, Dubaele S, et al. TFIIH contains a PH domain involved in DNA nucleotide excision repair. Nat Struct Mol Biol. 2004;11:616-22 pubmed..We solved its three-dimensional structure and found an unpredicted pleckstrin homology and phosphotyrosine binding (PH/PTB) domain, uncovering a new class of activity for this fold. ..
- Desgranges Z, Roy A. TFII-I: connecting mitogenic signals to cell cycle regulation. Cell Cycle. 2006;5:356-9 pubmed..We also discuss a potential role for TFII-I in DNA repair and how it might be involved in signal dependent DNA repair versus cell cycle. ..
- Itoh Y, Unzai S, Sato M, Nagadoi A, Okuda M, Nishimura Y, et al. Investigation of molecular size of transcription factor TFIIE in solution. Proteins. 2005;61:633-41 pubmed
- Sadowski I, Mitchell D. TFII-I and USF (RBF-2) regulate Ras/MAPK-responsive HIV-1 transcription in T cells. Eur J Cancer. 2005;41:2528-36 pubmed
- Desgranges Z, Ahn J, Lazebnik M, Ashworth T, Lee C, Pestell R, et al. Inhibition of TFII-I-dependent cell cycle regulation by p53. Mol Cell Biol. 2005;25:10940-52 pubmed
- Schultz P, Fribourg S, Poterszman A, Mallouh V, Moras D, Egly J. Molecular structure of human TFIIH. Cell. 2000;102:599-607 pubmed..Within the ring structure, p44 was flanked on either side by the XPB and XPD helicases. These observations provide us with a quartenary organizational model of TFIIH. ..
- Yudkovsky N, Ranish J, Hahn S. A transcription reinitiation intermediate that is stabilized by activator. Nature. 2000;408:225-9 pubmed..The scaffold is stabilized in the presence of the activator Gal4-VP16, but not Gal4-AH, suggesting a new role for some activators and Mediator in promoting high levels of transcription. ..
- Winkler G, Sugasawa K, Eker A, de Laat W, Hoeijmakers J. Novel functional interactions between nucleotide excision DNA repair proteins influencing the enzymatic activities of TFIIH, XPG, and ERCC1-XPF. Biochemistry. 2001;40:160-5 pubmed..These results point toward additional roles for TFIIH and ATP during NER distinct from a requirement for DNA unwinding in the regulation of the endonuclease activities of XPG and ERCC1-XPF. ..
- Wei W, Dorjsuren D, Lin Y, Qin W, Nomura T, Hayashi N, et al. Direct interaction between the subunit RAP30 of transcription factor IIF (TFIIF) and RNA polymerase subunit 5, which contributes to the association between TFIIF and RNA polymerase II. J Biol Chem. 2001;276:12266-73 pubmed..The exposed domain of RPB5 interacts with RAP30 of TFIIF and is important for the association between pol II and TFIIF. ..
- Zurita M, Merino C. The transcriptional complexity of the TFIIH complex. Trends Genet. 2003;19:578-84 pubmed..The second suggests that mutations in TFIIH produce specific phenotypes arising from differential interactions of this complex with different transcription regulatory factors. ..
- Zhang C, Yan H, Burton Z. Combinatorial control of human RNA polymerase II (RNAP II) pausing and transcript cleavage by transcription factor IIF, hepatitis delta antigen, and stimulatory factor II. J Biol Chem. 2003;278:50101-11 pubmed..In the presence of HDAg and SII, pausing is observed without stimulation of transcript cleavage, indicating that the EC can pause without backtracking beyond the pre-translocated state. ..
- Hakre S, Tussie Luna M, Ashworth T, Novina C, Settleman J, Sharp P, et al. Opposing functions of TFII-I spliced isoforms in growth factor-induced gene expression. Mol Cell. 2006;24:301-8 pubmed..Our results identify a unique growth factor signaling pathway controlled by opposing activities of two TFII-I spliced isoforms. ..
- Tapia Paez I, Tammimies K, Massinen S, Roy A, Kere J. The complex of TFII-I, PARP1, and SFPQ proteins regulates the DYX1C1 gene implicated in neuronal migration and dyslexia. FASEB J. 2008;22:3001-9 pubmed publisher..Furthermore, allelic differences in the promoter or 5' untranslated region of DYX1C1 may affect factor binding and thus regulation of the gene. ..
- Jawhari A, Laine J, Dubaele S, Lamour V, Poterszman A, Coin F, et al. p52 Mediates XPB function within the transcription/repair factor TFIIH. J Biol Chem. 2002;277:31761-7 pubmed..Taken together, our results show that the p52/Tfb2 subunit of TFIIH regulates the function of XPB through pair-wise interactions as described previously for p44 and XPD. ..
- Gaiser F, Tan S, Richmond T. Novel dimerization fold of RAP30/RAP74 in human TFIIF at 1.7 A resolution. J Mol Biol. 2000;302:1119-27 pubmed
- Ghazy M, Brodie S, Ammerman M, Ziegler L, Ponticelli A. Amino acid substitutions in yeast TFIIF confer upstream shifts in transcription initiation and altered interaction with RNA polymerase II. Mol Cell Biol. 2004;24:10975-85 pubmed..These results provide direct evidence for the involvement of S. cerevisiae TFIIF in the mechanism of transcription start site utilization and support the view that a TFIIF-RNA polymerase II interaction is a determinant in this process. ..
- 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 pubmed..The TFIIF subunit Tfg1 was found in close proximity to the TFIIB B finger, linker, and core domains, suggesting that these two factors closely cooperate during initiation. ..
- Kamada K, De Angelis J, Roeder R, Burley S. Crystal structure of the C-terminal domain of the RAP74 subunit of human transcription factor IIF. Proc Natl Acad Sci U S A. 2001;98:3115-20 pubmed..RAP74 has been shown to interact with the TFIIF-associated C-terminal domain phosphatase FCP1, and a putative phosphatase binding site has been identified within the RAP74 winged-helix domain. ..
- Jawhari A, Boussert S, Lamour V, Atkinson R, Kieffer B, Poch O, et al. Domain architecture of the p62 subunit from the human transcription/repair factor TFIIH deduced by limited proteolysis and mass spectrometry analysis. Biochemistry. 2004;43:14420-30 pubmed..The approach used in this study is general and can be straightforwardly applied to other multidomain proteins and/or multiprotein assemblies. ..
- Spangler L, Wang X, Conaway J, Conaway R, Dvir A. TFIIH action in transcription initiation and promoter escape requires distinct regions of downstream promoter DNA. Proc Natl Acad Sci U S A. 2001;98:5544-9 pubmed
- Ranish J, Hahn S, Lu Y, Yi E, Li X, Eng J, et al. Identification of TFB5, a new component of general transcription and DNA repair factor IIH. Nat Genet. 2004;36:707-13 pubmed..The identification of a new, evolutionarily conserved, core TFIIH subunit is essential for our understanding of TFIIH function in transcription, DNA repair and human disease. ..
- Funk J, Nedialkov Y, Xu D, Burton Z. A key role for the alpha 1 helix of human RAP74 in the initiation and elongation of RNA chains. J Biol Chem. 2002;277:46998-7003 pubmed..The molecular target of the alpha1 helix remains unknown, but our studies refocus attention on this important functional motif of TFIIF. ..
- Edelmann L, Prosnitz A, Pardo S, Bhatt J, Cohen N, Lauriat T, et al. An atypical deletion of the Williams-Beuren syndrome interval implicates genes associated with defective visuospatial processing and autism. J Med Genet. 2007;44:136-43 pubmed..Symptoms of autism in this case may be due to deletion of additional genes outside the typical WBS interval or remote effects on gene expression at other loci. ..
- Ren D, Lei L, Burton Z. A region within the RAP74 subunit of human transcription factor IIF is critical for initiation but dispensable for complex assembly. Mol Cell Biol. 1999;19:7377-87 pubmed..Negative DNA supercoiling partially compensates for the defects of TFIIF mutants in initiation, indicating that TFIIF may help to untwist the DNA helix for initiation. ..
- Di Lello P, Nguyen B, Jones T, Potempa K, Kobor M, Legault P, et al. NMR structure of the amino-terminal domain from the Tfb1 subunit of TFIIH and characterization of its phosphoinositide and VP16 binding sites. Biochemistry. 2005;44:7678-86 pubmed..These results provide new information about the recognition of phosphoinositides by PH domains, and point to a potential role for phosphoinositides in VP16 regulation. ..
- Giglia Mari G, Coin F, Ranish J, Hoogstraten D, Theil A, Wijgers N, et al. A new, tenth subunit of TFIIH is responsible for the DNA repair syndrome trichothiodystrophy group A. Nat Genet. 2004;36:714-9 pubmed..The identification of a new evolutionarily conserved subunit of TFIIH implicated in TTD-A provides insight into TFIIH function in transcription, DNA repair and human disease. ..
- Watanabe T, Hayashi K, Tanaka A, Furumoto T, Hanaoka F, Ohkuma Y. The carboxy terminus of the small subunit of TFIIE regulates the transition from transcription initiation to elongation by RNA polymerase II. Mol Cell Biol. 2003;23:2914-26 pubmed..This is an important clue for elucidating the molecular mechanisms involved in the transition stage. ..
- Keriel A, Stary A, Sarasin A, Rochette Egly C, Egly J. XPD mutations prevent TFIIH-dependent transactivation by nuclear receptors and phosphorylation of RARalpha. Cell. 2002;109:125-35 pubmed..Thus, we demonstrate that the cdk7 kinase of TFIIH phosphorylates the nuclear receptor, then allowing ligand-dependent control of the activation of the hormone-responsive genes. ..
- Elmendorf B, Shilatifard A, Yan Q, Conaway J, Conaway R. Transcription factors TFIIF, ELL, and Elongin negatively regulate SII-induced nascent transcript cleavage by non-arrested RNA polymerase II elongation intermediates. J Biol Chem. 2001;276:23109-14 pubmed
- Kim T, Ebright R, Reinberg D. Mechanism of ATP-dependent promoter melting by transcription factor IIH. Science. 2000;288:1418-22 pubmed..We propose that IIH functions as a molecular wrench: rotating downstream DNA relative to fixed upstream protein-DNA interactions, thereby generating torque on, and melting, the intervening DNA. ..
- Tassabehji M, Hammond P, Karmiloff Smith A, Thompson P, Thorgeirsson S, Durkin M, et al. GTF2IRD1 in craniofacial development of humans and mice. Science. 2005;310:1184-7 pubmed..We propose a mechanism of cumulative dosage effects of duplicated and diverged genes applicable to other human chromosomal disorders. ..
- Jawhari A, Uhring M, De Carlo S, Crucifix C, Tocchini Valentini G, Moras D, et al. Structure and oligomeric state of human transcription factor TFIIE. EMBO Rep. 2006;7:500-5 pubmed..Finally, a model for the quaternary architecture of the complex is proposed that provides a structural framework to discuss the function of TFIIE in the context of RNA polymerase II transcription initiation. ..
- Kabani M, Michot K, Boschiero C, Werner M. Anc1 interacts with the catalytic subunits of the general transcription factors TFIID and TFIIF, the chromatin remodeling complexes RSC and INO80, and the histone acetyltransferase complex NuA3. Biochem Biophys Res Commun. 2005;332:398-403 pubmed..We show that Anc1 is required for growth on galactose as the sole carbon source, and that it is recruited to the UAS of the GAL1 gene after induction. ..
- Meinhart A, Blobel J, Cramer P. An extended winged helix domain in general transcription factor E/IIE alpha. J Biol Chem. 2003;278:48267-74 pubmed publisher..Homology modeling shows that the TFE domain is conserved in TFIIE alpha, including the potential functional surfaces...
- Hirota H, Matsuoka R, Chen X, Salandanan L, Lincoln A, Rose F, et al. Williams syndrome deficits in visual spatial processing linked to GTF2IRD1 and GTF2I on chromosome 7q11.23. Genet Med. 2003;5:311-21 pubmed..Combining the molecular analysis with the cognitive results suggest that the genes GTF2IRD1 and GTF2I contribute to deficits on visual spatial functioning. ..
- Bagby S, Mal T, Liu D, Raddatz E, Nakatani Y, Ikura M. TFIIA-TAF regulatory interplay: NMR evidence for overlapping binding sites on TBP. FEBS Lett. 2000;468:149-54 pubmed..Together with previous mutational and biochemical data, our NMR results indicate that subdomain II augments subdomain I-mediated inhibition of TBP function by blocking TBP-TFIIA interaction. ..
- Esnault C, Ghavi Helm Y, Brun S, Soutourina J, Van Berkum N, Boschiero C, et al. Mediator-dependent recruitment of TFIIH modules in preinitiation complex. Mol Cell. 2008;31:337-46 pubmed publisher..We conclude that the Mediator head module plays a critical role in TFIIH and TFIIE recruitment to the PIC. We identify steps in PIC formation that suggest a branched assembly pathway. ..