Genomes and Genes
general transcription factors
Summary: Transcription factors that form transcription initiation complexes on DNA, bind to specific DNA-DIRECTED RNA POLYMERASES and are required to initiate transcription. Although their binding may be localized to distinct sequence and structural motifs within the DNA they are considered non-specific with regard to the specific gene being transcribed.
- Langer D, Zillig W. Putative tfIIs gene of Sulfolobus acidocaldarius encoding an archaeal transcription elongation factor is situated directly downstream of the gene for a small subunit of DNA-dependent RNA polymerase. Nucleic Acids Res. 1993;21:2251 pubmed
- Ito T, Xu Q, Takeuchi H, Kubo T, Natori S. Spermatocyte-specific expression of the gene for mouse testis-specific transcription elongation factor S-II. FEBS Lett. 1996;385:21-4 pubmed..RT-PCR experiments using testis RNA from W/Wv mutant mice also suggested that SII-T1 is a specific transcription elongation factor essential for spermatogenesis. ..
- Opalka N, Chlenov M, Chacon P, Rice W, Wriggers W, Darst S. Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase. Cell. 2003;114:335-45 pubmed..Mutational studies confirm that these positions are critical for Gre factor function. ..
- Labhart P, Morgan G. Identification of novel genes encoding transcription elongation factor TFIIS (TCEA) in vertebrates: conservation of three distinct TFIIS isoforms in frog, mouse, and human. Genomics. 1998;52:278-88 pubmed..Phylogenetic analysis of TFIIS sequences demonstrates the ancient origins of the three vertebrate isoforms, although they appeared functionally equivalent in in vitro RNA cleavage assays. ..
- Perez Amador M, Lidder P, Johnson M, Landgraf J, Wisman E, Green P. New molecular phenotypes in the dst mutants of Arabidopsis revealed by DNA microarray analysis. Plant Cell. 2001;13:2703-17 pubmed..Cluster analysis of genes altered in dst1 revealed new coexpression patterns that prompt new hypotheses regarding the nature of the dst1 mutation and a possible role of the DST-mediated mRNA decay pathway in plants. ..
- Kugawa F, Aoki M. Genomic cloning of Xenopus TFIIS (TCEA1) and identification of its transcription start site. DNA Seq. 2002;13:55-60 pubmed
- Oh Y, Lee S, Yoon J, Han K, Baek K. Promoter analysis of the Drosophila melanogaster gene encoding transcription elongation factor TFIIS. Biochim Biophys Acta. 2001;1518:276-81 pubmed..melanogaster TFIIS gene. ..
- Zhang J, Li E, Olsen G. Protein-coding gene promoters in Methanocaldococcus (Methanococcus) jannaschii. Nucleic Acids Res. 2009;37:3588-601 pubmed publisher..Relative binding affinity for general transcription factors was measured for 12 of these promoters by competition electrophoretic mobility shift assays...
- Labhart P. Transcript cleavage in an RNA polymerase I elongation complex. Evidence for a dissociable activity similar to but distinct from TFIIS. J Biol Chem. 1997;272:9055-61 pubmed..The predicted amino acid sequences of the present and previously identified Xenopus TFIIS are less than 65% conserved. Thus, like mammalian species, Xenopus has at least two highly divergent forms of TFIIS. ..
- Qian X, Jeon C, Yoon H, Agarwal K, Weiss M. Structure of a new nucleic-acid-binding motif in eukaryotic transcriptional elongation factor TFIIS. Nature. 1993;365:277-9 pubmed publisher..This new structure, designated the Zn ribbon, extends the repertoire of Zn-mediated peptide architectures and highlights the growing recognition of the beta-sheet as a motif of nucleic-acid recognition...
- Umehara T, Kida S, Yamamoto T, Horikoshi M. Isolation and characterization of a cDNA encoding a new type of human transcription elongation factor S-II. Gene. 1995;167:297-302 pubmed..The significance of tissue-specific S-II molecules for the regulation of transcription elongation is discussed. ..
- Krogan N, Kim M, Ahn S, Zhong G, Kobor M, Cagney G, et al. RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. Mol Cell Biol. 2002;22:6979-92 pubmed..Spt5, Spt6, and Iws1 are phosphorylated on consensus CKII sites in vivo, conceivably by the Chd1/CKII associated with Spt16/Pob3. All the elongation factors but Elongator copurified with RNAPII. ..
- Perez Rueda E, Collado Vides J, Segovia L. Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea. Comput Biol Chem. 2004;28:341-50 pubmed..This analysis provides a framework for discussing the selective forces directing the evolution of the transcriptional machinery in prokaryotes. ..
- Pijnappel W, Timmers H. Dubbing SAGA unveils new epigenetic crosstalk. Mol Cell. 2008;29:152-4 pubmed publisher..2008; Zhao et al., 2008) provide compelling evidence that targeted deubiquitylation of histones is intimately linked to transcription activation, epigenetic regulation, and cancer progression. ..
- Yeh C, Shatkin A. A HeLa-cell-encoded p21 is homologous to transcription elongation factor SII. Gene. 1994;143:285-7 pubmed..The deduced amino-acid sequence of p21 indicates that it is hydrophilic, basic and contains nuclear localization signals, as well as multiple consensus phosphorylation sites. ..
- Lee K, Park J, Sohn T, Kim S, Rhee J, Kim J. Interaction of polymorphisms in the interleukin 1B-31 and general transcription factor 2A1 genes on the susceptibility to gastric cancer. Cytokine. 2007;38:96-100 pubmed..Our results also suggest that an additional host genetic factor acting epistatically may differentially contribute to the histogenesis of the diffuse and intestinal subtypes. ..
- Martina J, Bonangelino C, Aguilar R, Bonifacino J. Stonin 2: an adaptor-like protein that interacts with components of the endocytic machinery. J Cell Biol. 2001;153:1111-20 pubmed..These observations suggest that stonin 2 is a novel component of the general endocytic machinery. ..
- Pan G, Aso T, Greenblatt J. Interaction of elongation factors TFIIS and elongin A with a human RNA polymerase II holoenzyme capable of promoter-specific initiation and responsive to transcriptional activators. J Biol Chem. 1997;272:24563-71 pubmed..This holoenzyme contained nearstoichiometric amounts of all the general transcription factors, TFIIB, TFIID (TBP + TAFIIs), TFIIE, TFIIF, and TFIIH, required to accurately initiate transcription ..
- Chedin S, Riva M, Schultz P, Sentenac A, Carles C. The RNA cleavage activity of RNA polymerase III is mediated by an essential TFIIS-like subunit and is important for transcription termination. Genes Dev. 1998;12:3857-71 pubmed..The integration of TFIIS function into a specific Pol III subunit may stem from the opposite requirements of Pol III and Pol II in terms of transcript length and termination efficiency. ..
- Taira Y, Kubo T, Natori S. Participation of transcription elongation factor XSII-K1 in mesoderm-derived tissue development in Xenopus laevis. J Biol Chem. 2000;275:32011-5 pubmed..This is the first demonstration that the regulation at the level of transcription elongation is included in the development of mesoderm-derived tissues. ..
- Davie J, Kane C. Genetic interactions between TFIIS and the Swi-Snf chromatin-remodeling complex. Mol Cell Biol. 2000;20:5960-73 pubmed..The detection of these genetic interactions provides another functional link between the Swi-Snf complex and the elongation machinery. ..
- Fiedler U, Timmers H. Analysis of the open region of RNA polymerase II transcription complexes in the early phase of elongation. Nucleic Acids Res. 2001;29:2706-14 pubmed..These findings are discussed in the light of the recently determined structures for RNA polymerases. ..
- Archambault J, Lacroute F, Ruet A, Friesen J. Genetic interaction between transcription elongation factor TFIIS and RNA polymerase II. Mol Cell Biol. 1992;12:4142-52 pubmed..In addition to implicating a region of the largest subunit of RNAPII in the process of transcript elongation, our observations provide in vivo evidence that TFIIS is involved in transcription by RNAPII. ..
- Kalogeraki V, Tornaletti S, Hanawalt P. Transcription arrest at a lesion in the transcribed DNA strand in vitro is not affected by a nearby lesion in the opposite strand. J Biol Chem. 2003;278:19558-64 pubmed..Our results additionally indicate that the sequence context of a CPD affects the efficiency of T7 RNAP arrest more significantly than that of RNAP II. ..
- Männistö R, Grahn A, Bamford D, Bamford J. Transcription of bacteriophage PM2 involves phage-encoded regulators of heterologous origin. J Bacteriol. 2003;185:3278-87 pubmed..P14, the transcription activator for the structural genes, has a zinc finger motif homologous to archaeal and eukaryotic TFIIS-type regulatory factors...
- Saso K, Ito T, Natori S, Sekimizu K. Identification of a novel tissue-specific transcriptional activator FESTA as a protein that interacts with the transcription elongation factor S-II. J Biochem. 2003;133:493-500 pubmed..This study is the first report of a transcriptional activator that directly interacts with S-II and contains a transcriptional activation domain that cooperates with S-II via direct interaction. ..
- Otero G, Fellows J, Li Y, de Bizemont T, Dirac A, Gustafsson C, et al. Elongator, a multisubunit component of a novel RNA polymerase II holoenzyme for transcriptional elongation. Mol Cell. 1999;3:109-18 pubmed..Our data indicate that the transition from transcriptional initiation to elongation involves an exchange of the multiprotein mediator complex for elongator in a reaction coupled to CTD hyperphosphorylation. ..
- Krogan N, Keogh M, Datta N, Sawa C, Ryan O, Ding H, et al. A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Mol Cell. 2003;12:1565-76 pubmed..We show that recruitment of Htz1 to chromatin requires the SWR-C. Moreover, like Htz1 and Bdf1, the SWR-C promotes gene expression near silent heterochromatin. ..
- De Planell Saguer M, Schroeder D, Rodicio M, Cox G, Mourelatos Z. Biochemical and genetic evidence for a role of IGHMBP2 in the translational machinery. Hum Mol Genet. 2009;18:2115-26 pubmed publisher..Our findings strongly suggest that IGHMBP2 is a component of the translational machinery and that these components can be manipulated genetically to suppress motor neuron degeneration. ..
- Tschochner H. A novel RNA polymerase I-dependent RNase activity that shortens nascent transcripts from the 3' end. Proc Natl Acad Sci U S A. 1996;93:12914-9 pubmed..Shortened transcripts that remained associated within the ternary complexes were capable of resuming RNA chain elongation. Possible functions of the nuclease for transcript elongation or termination are discussed. ..
- Holland L, Gauthier L, Bell Rogers P, Yankulov K. Distinct parts of minichromosome maintenance protein 2 associate with histone H3/H4 and RNA polymerase II holoenzyme. Eur J Biochem. 2002;269:5192-202 pubmed..also showed that bacterially expressed amino acids 169-212 of MCM2 associate with pol II and several general transcription factors in vitro...
- Gnatt A. Elongation by RNA polymerase II: structure-function relationship. Biochim Biophys Acta. 2002;1577:175-90 pubmed..Structural studies of RNA polymerases are described below within the context of the process of transcription elongation, its regulation and function. ..
- McNeilly J, Jimenez L, Clay M, MacNee W, Howe A, Heal M, et al. Soluble transition metals in welding fumes cause inflammation via activation of NF-kappaB and AP-1. Toxicol Lett. 2005;158:152-7 pubmed
- Reines D, Chamberlin M, Kane C. Transcription elongation factor SII (TFIIS) enables RNA polymerase II to elongate through a block to transcription in a human gene in vitro. J Biol Chem. 1989;264:10799-809 pubmed..A homogeneous preparation of calf thymus SII can also provide this activity in trans. This factor may facilitate passage of the RNA polymerase II transcription complex through such intragenic sites in cellular genes in vivo. ..
- Kulish D, Struhl K. TFIIS enhances transcriptional elongation through an artificial arrest site in vivo. Mol Cell Biol. 2001;21:4162-8 pubmed
- Shimoaraiso M, Nakanishi T, Kubo T, Natori S. Transcription elongation factor S-II confers yeast resistance to 6-azauracil by enhancing expression of the SSM1 gene. J Biol Chem. 2000;275:29623-7 pubmed..These results indicate that S-II confers yeast resistance to 6-azauracil by stimulating transcription elongation of the SSM1 gene. ..
- Reines D, Conaway J, Conaway R. The RNA polymerase II general elongation factors. Trends Biochem Sci. 1996;21:351-5 pubmed..of eukaryotic messenger RNA by RNA polymerase II is governed by the concerted action of a set of general transcription factors that control the activity of polymerase during both the initiation and elongation stages of ..
- Yeh C, Zong W, Shatkin A. The Ser36-Ser37 pair in HeLa nuclear protein p21/SIIR mediates Ser/Thr phosphorylation and is essential for Rous sarcoma virus long terminal repeat repression. J Biol Chem. 1995;270:25313-5 pubmed..The single tyrosine (Tyr155) in p21/SIIR was not detectably phosphorylated in transfected COS-1 cells, suggesting that the Ser36-Ser37 pair mediates Ser/Thr phosphorylation of p21/SIIR and is critical for LTR repression function. ..
- Keyamura K, Fujikawa N, Ishida T, Ozaki S, Su etsugu M, Fujimitsu K, et al. The interaction of DiaA and DnaA regulates the replication cycle in E. coli by directly promoting ATP DnaA-specific initiation complexes. Genes Dev. 2007;21:2083-99 pubmed..These results suggest an essential role for DiaA in the promotion of replication initiation in a cell cycle coordinated manner. ..
- Gileadi O, Feaver W, Kornberg R. Cloning of a subunit of yeast RNA polymerase II transcription factor b and CTD kinase. Science. 1992;257:1389-92 pubmed..Photoaffinity labeling with 3'-O-(4-benzoyl)benzoyl-ATP (adenosine triphosphate) identified an ATP-binding site in the 85-kilodalton polypeptide, suggesting that the 85-kilodalton subunit contains the catalytic domain of the kinase. ..
- Lindstrom D, Hartzog G. Genetic interactions of Spt4-Spt5 and TFIIS with the RNA polymerase II CTD and CTD modifying enzymes in Saccharomyces cerevisiae. Genetics. 2001;159:487-97 pubmed..These results suggest that the CTD plays a key role in modulating elongation in vivo and that at least a subset of elongation factors are dependent upon the CTD for their normal function. ..
- 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
- Selby C, Sancar A. Cockayne syndrome group B protein enhances elongation by RNA polymerase II. Proc Natl Acad Sci U S A. 1997;94:11205-9 pubmed..Thus a deficiency in transcription elongation may contribute to the CS phenotype...
- DiMarco S, Glover T, Miller D, Reines D, Warren S. Transcription elongation factor SII (TCEA) maps to human chromosome 3p22 --> p21.3. Genomics. 1996;36:185-8 pubmed..3. ..
- Han Q, Hou X, Su D, Pan L, Duan J, Cui L, et al. hELP3 subunit of the Elongator complex regulates the transcription of HSP70 gene in human cells. Acta Biochim Biophys Sin (Shanghai). 2007;39:453-61 pubmed..Data presented in this report provide further insight and direct evidence of the functions of hELP3 in HSP70-2 gene transcriptional elongation in human cells. ..
- Verhage R, Heyn J, van de Putte P, Brouwer J. Transcription elongation factor S-II is not required for transcription-coupled repair in yeast. Mol Gen Genet. 1997;254:284-90 pubmed..Hence, transcription-coupled repair is fully functional in yeast cells lacking the gene encoding S-II. Furthermore, S-II is not required for the Rad26-independent residual transcription-coupled repair in vivo. ..
- Hirashima S, Hirai H, Nakanishi Y, Natori S. Molecular cloning and characterization of cDNA for eukaryotic transcription factor S-II. J Biol Chem. 1988;263:3858-63 pubmed..The results of analysis of the genomic structure suggested that the polymorphism of mRNA may be due to alternative splicing, or differences in initiation or termination of transcription. ..
- Chen H, England L, Kane C. Characterization of a HeLa cDNA clone encoding the human SII protein, an elongation factor for RNA polymerase II. Gene. 1992;116:253-8 pubmed..A comparison of deduced amino acid sequences for SII-related proteins from a variety of eukaryotes demonstrates very high similarity, especially within the C-terminal domain. ..
- Ishiguro A, Nogi Y, Hisatake K, Muramatsu M, Ishihama A. The Rpb6 subunit of fission yeast RNA polymerase II is a contact target of the transcription elongation factor TFIIS. Mol Cell Biol. 2000;20:1263-70 pubmed..Taken together, the results lead us to propose that Rpb6 plays a role in the interaction between RNA polymerase II and the transcription elongation factor TFIIS. ..
- Taira Y, Kubo T, Natori S. Molecular cloning of cDNA and tissue-specific expression of the gene for SII-K1, a novel transcription elongation factor SII. Genes Cells. 1998;3:289-96 pubmed..This factor was expressed exclusively in the heart, liver, kidney and skeletal muscle. During mouse embryonic development, no significant expression of the SII-K1 gene was detected before the formation of these tissues. ..
- Plant K, Hair A, Morgan G. Genes encoding isoforms of transcription elongation factor TFIIS in Xenopus and the use of multiple unusual RNA processing signals. Nucleic Acids Res. 1996;24:3514-21 pubmed..Utilization of multiple unusual processing signals may make the generation of mature xTFIIS.o mRNAs inefficient and the possible regulatory consequences of this are discussed. ..
- Trembley J, Hu D, Hsu L, Yeung C, Slaughter C, Lahti J, et al. PITSLRE p110 protein kinases associate with transcription complexes and affect their activity. J Biol Chem. 2002;277:2589-96 pubmed..Together, these data strongly suggest that PITSLRE protein kinases participate in a signaling pathway that potentially regulates or links transcription and RNA processing events. ..