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He S, You JJ, Liang XF, Zhang ZL, Zhang YP. Transcriptome sequencing and metabolome analysis of food habits domestication from live prey fish to artificial diets in mandarin fish (Siniperca chuatsi). BMC Genomics 2021; 22:129. [PMID: 33618656 PMCID: PMC7898776 DOI: 10.1186/s12864-021-07403-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 01/22/2021] [Indexed: 12/20/2022] Open
Abstract
Background As economical traits, food habits domestication can reduce production cost in aquaculture. However, the molecular mechanism underlying food habits domestication has remained elusive. Mandarin fish (Siniperca chuatsi) only feed on live prey fish and refuse artificial diets. In the present study, we domesticated mandarin fish to feed on artificial diets. The two groups were obtained, the fish did not eat artificial diets or ate artificial diets during all of the three domestication processes, named Group W or X, respectively. Results Using transcriptome and metabolome analysis, we investigated the differentially expressed genes and metabolites between the two groups, and found three common pathways related to food habit domestication, including retinol metabolism, glycerolipid metabolism, and biosynthesis of unsaturated fatty acids pathways. Furthermore, the western blotting and bisulfite sequencing PCR analysis were performed. The gene expression of TFIIF and histone methyltransferase ezh1 were significantly increased and decreased in the fish of Group X, respectively. The total DNA methylation levels of TFIIF gene and tri-methylation of histone H3 at lysine 27 (H3K27me3) were significantly higher and lower in the fish of Group X, respectively. Conclusion It was speculated that mandarin fish which could feed on artificial diets, might be attributed to the lower expression of ezh1, resulting in the decreased level of H3K27me3 and increased level of DNA methylation of TFIIF gene. The high expression of TFIIF gene might up-regulate the expression of genes in retinol metabolism, glycerolipid metabolism and glycerophosphoric metabolism pathways. Our study indicated the relationship between the methylation of DNA and histone and food habits domestication, which might be a novel molecular mechanism of food habits domestication in animals.
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Affiliation(s)
- Shan He
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, 430070, Hubei, China.,Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, 430070, China.,Anhui Province Key Laboratory of Aquaculture & Stock Enhancement, Fishery Institute of Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Jun-Jie You
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, 430070, Hubei, China.,Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, 430070, China.,Anhui Province Key Laboratory of Aquaculture & Stock Enhancement, Fishery Institute of Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Xu-Fang Liang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, 430070, Hubei, China. .,Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, 430070, China.
| | - Zhi-Lu Zhang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, 430070, Hubei, China.,Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, 430070, China
| | - Yan-Peng Zhang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, 430070, Hubei, China.,Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, 430070, China
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Greber BJ, Nogales E. The Structures of Eukaryotic Transcription Pre-initiation Complexes and Their Functional Implications. Subcell Biochem 2019; 93:143-192. [PMID: 31939151 DOI: 10.1007/978-3-030-28151-9_5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transcription is a highly regulated process that supplies living cells with coding and non-coding RNA molecules. Failure to properly regulate transcription is associated with human pathologies, including cancers. RNA polymerase II is the enzyme complex that synthesizes messenger RNAs that are then translated into proteins. In spite of its complexity, RNA polymerase requires a plethora of general transcription factors to be recruited to the transcription start site as part of a large transcription pre-initiation complex, and to help it gain access to the transcribed strand of the DNA. This chapter reviews the structure and function of these eukaryotic transcription pre-initiation complexes, with a particular emphasis on two of its constituents, the multisubunit complexes TFIID and TFIIH. We also compare the overall architecture of the RNA polymerase II pre-initiation complex with those of RNA polymerases I and III, involved in transcription of ribosomal RNA and non-coding RNAs such as tRNAs and snRNAs, and discuss the general, conserved features that are applicable to all eukaryotic RNA polymerase systems.
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Affiliation(s)
- Basil J Greber
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA.
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Eva Nogales
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
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3
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Geiger SR, Lorenzen K, Schreieck A, Hanecker P, Kostrewa D, Heck AJ, Cramer P. RNA Polymerase I Contains a TFIIF-Related DNA-Binding Subcomplex. Mol Cell 2010; 39:583-94. [DOI: 10.1016/j.molcel.2010.07.028] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 06/15/2010] [Accepted: 06/29/2010] [Indexed: 01/09/2023]
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4
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Chen ZA, Jawhari A, Fischer L, Buchen C, Tahir S, Kamenski T, Rasmussen M, Lariviere L, Bukowski-Wills JC, Nilges M, Cramer P, Rappsilber J. Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry. EMBO J 2010; 29:717-26. [PMID: 20094031 PMCID: PMC2810376 DOI: 10.1038/emboj.2009.401] [Citation(s) in RCA: 316] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Accepted: 12/10/2009] [Indexed: 11/09/2022] Open
Abstract
Higher-order multi-protein complexes such as RNA polymerase II (Pol II) complexes with transcription initiation factors are often not amenable to X-ray structure determination. Here, we show that protein cross-linking coupled to mass spectrometry (MS) has now sufficiently advanced as a tool to extend the Pol II structure to a 15-subunit, 670 kDa complex of Pol II with the initiation factor TFIIF at peptide resolution. The N-terminal regions of TFIIF subunits Tfg1 and Tfg2 form a dimerization domain that binds the Pol II lobe on the Rpb2 side of the active centre cleft near downstream DNA. The C-terminal winged helix (WH) domains of Tfg1 and Tfg2 are mobile, but the Tfg2 WH domain can reside at the Pol II protrusion near the predicted path of upstream DNA in the initiation complex. The linkers between the dimerization domain and the WH domains in Tfg1 and Tfg2 are located to the jaws and protrusion, respectively. The results suggest how TFIIF suppresses non-specific DNA binding and how it helps to recruit promoter DNA and to set the transcription start site. This work establishes cross-linking/MS as an integrated structure analysis tool for large multi-protein complexes.
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Affiliation(s)
- Zhuo Angel Chen
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, The University of Edinburgh, Edinburgh, UK
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5
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Ha E, Han E, Park HJ, Kim HJ, Hong MS, Hong SJ, Yoon KS, Kang I, Cho YH, Chung JH, Yim SV, Baik HH. Microarray analysis of transcription factor gene expression in melatonin-treated human peripheral blood mononuclear cells. J Pineal Res 2006; 40:305-11. [PMID: 16635017 DOI: 10.1111/j.1600-079x.2006.00317.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The existence of specific melatonin-binding sites in lymphoid cells led to the discovery of signal transduction pathway for melatonin in human lymphocytes and immunomodulatory role of melatonin in immune cells. In recent years, transcriptional regulation of melatonin on various transcription factors has been demonstrated. Therefore, this study was designed to assess by cDNA microarray analysis the regulatory effects of melatonin on transcription factors in human peripheral blood mononuclear cells (PBMCs). Forty-six genes were upregulated and 23 were downregulated more than twofold in melatonin-treated PBMCs. Of the more than twofold upregulated transcription factor genes, homeo box A4 (HOXA4), forkhead box O1A (FOXO1A), transcription elongation factor B (SIII), polypeptide 3 (TCEB3), and peroxisome proliferative activated receptor delta (PPARD) were identified. Of the more than twofold downregulated genes, PHD finger protein 15 (PHF15) and zinc finger protein 33a (ZNF33A) were identified. In summary, identification of these genes by cDNA microarray analysis in response to melatonin administration may provide a foundation for further studies on the function of melatonin in human PBMCs.
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Affiliation(s)
- Eunyoung Ha
- Department of Biochemisty, Kohwang Medical Research Institute, College of Medicine, Kyung Hee University, Seoul, Korea
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6
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Abstract
Recent X-ray and cryo-electron microscopy studies have provided information about the basal eukaryotic transcription machinery and about Mediator, the complex involved in transcription regulation during initiation. On the basis of this structural information, a model describing the minimal transcription complex and its interaction with Mediator has been proposed. The model provides insight into the possible mechanisms of transcription initiation and regulation.
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Affiliation(s)
- Francisco J Asturias
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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7
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Chung WH, Craighead JL, Chang WH, Ezeokonkwo C, Bareket-Samish A, Kornberg RD, Asturias FJ. RNA Polymerase II/TFIIF Structure and Conserved Organization of the Initiation Complex. Mol Cell 2003; 12:1003-13. [PMID: 14580350 DOI: 10.1016/s1097-2765(03)00387-3] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The structure of an RNA polymerase II/general transcription factor TFIIF complex was determined by cryo-electron microscopy and single particle analysis. Density due to TFIIF was not concentrated in one area but rather was widely distributed across the surface of the polymerase. The largest subunit of TFIIF interacted with the dissociable Rpb4/Rpb7 polymerase subunit complex and with the mobile "clamp." The distribution of the second largest subunit of TFIIF was very similar to that previously reported for the sigma subunit in the bacterial RNA polymerase holoenzyme, consisting of a series of globular domains extending along the polymerase active site cleft. This result indicates that the second TFIIF subunit is a true structural homolog of the bacterial sigma factor and reveals an important similarity of the transcription initiation mechanism between bacteria and eukaryotes. The structure of the RNAPII/TFIIF complex suggests a model for the organization of a minimal transcription initiation complex.
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Affiliation(s)
- Wen-Hsiang Chung
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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8
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Wei W, Gu JX, Zhu CQ, Sun FY, Dorjsuren D, Lin Y, Murakami S. Interaction with general transcription factor IIF (TFIIF) is required for the suppression of activated transcription by RPB5-mediating protein (RMP). Cell Res 2003; 13:111-20. [PMID: 12737519 DOI: 10.1038/sj.cr.7290155] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
RMP was reported to regulate transcription via competing with HBx to bind the general transcription factor IIB (TFIIB) and interacting with RPB5 subunit of RNA polymerase II as a corepressor of transcription regulator. However, our present research uncovered that RMP also regulates the transcription through interaction with the general transcription factors IIF (TFIIF), which assemble in the preinitiation complex and function in both transcription initiation and elongation. With in vitro pull-down assay and Far-Western analysis, we demonstrated that RMP could bind with bacterially expressed recombinant RAP30 and RAP74 of TFIIF subunits. In the immunoprecipitation assay in COS1 cells cotransfected with FLAG-tagged RMP or its mutants, GST-fused RAP30 and RAP74 were co-immunoprecipitated with RMP in approximately equal molar ratio, which suggests that RAP30 and RAP74 interact with RMP as a TFIIF complex. Interestingly both RAP30 and RAP74 interact with the same domain (D5) of the C-terminal RMP of 118-amino-acid residuals which overlaps with its TFIIB-binding domain. Internal deletion of D5 region of RMP abolished its binding ability with both subunits of TFIIF, while D5 domain alone was sufficient to interact with TFIIF subunits. The result of luciferase assay showed that overexpression of RMP, but not the mutant RMP lacking D5 region, suppressed the transcription activated by Gal-VP16, suggesting that interaction with TFIIF is required for RMP to suppress the activated transcription. The interaction between RMP and TFIIF may be an additional passway for RMP to regulate the transcription, or alternatively TFIIF may cooperate with RPB5 and TFIIB for the corepressor function of RMP.
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Affiliation(s)
- Wenxiang Wei
- National Key Laboratory of Medical Neurobiology, Fudan University, 138 Yi Xue Yuan Road, Shanghai 200032, China.
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9
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Gaiser F, Tan S, Richmond TJ. Novel dimerization fold of RAP30/RAP74 in human TFIIF at 1.7 A resolution. J Mol Biol 2000; 302:1119-27. [PMID: 11183778 DOI: 10.1006/jmbi.2000.4110] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
General transcription factor IIF (TFIIF) is required for transcription by RNA polymerase II; it consists minimally of a heterodimer of RNA polymerase-associated proteins RAP30 and RAP74. According to solution and mutagenesis studies, the multiple domains of RAP30 and RAP74 bind PolII, TFIIB, TAF250 and DNA in interactions that are essential for transcription initiation and elongation. The X-ray structure of the RAP30/RAP74 interaction domains at 1.7 A resolution reveals a novel "triple barrel" dimerization fold and suggests with mutant data that interactions with the transcription apparatus are mediated not only by this tripartite beta-barrel, but also via flexible loops and alpha and beta-structures extending from it.
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Affiliation(s)
- F Gaiser
- ETH Zürich, Institut fr Molekularbiologie und Biophysik, Zürich, Switzerland
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10
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Thompson NE, Burgess RR. Immunoaffinity purification of the RAP30 subunit of human transcription factor IIF. Protein Expr Purif 1999; 17:260-6. [PMID: 10545274 DOI: 10.1006/prep.1999.1128] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
RAP30, an RNA polymerase-associated protein (RAP) of approximately 30 kDa, is a component of the eukaryotic general transcription factor IIF (TFIIF). We have isolated a monoclonal antibody (MAb) that can be used to purify RAP30 under nondenaturing conditions. This MAb (designated 1RAP1) is a unique type of MAb that we have designated "polyol-responsive MAb." Polyol-responsive MAbs are high-affinity antibodies that release antigen in a buffer containing a low-molecular-weight polyhydroxylated compound (polyol) and a nonchaotropic salt. RAP30, contained on pET11d, was expressed in Escherichia coli by culturing and inducing protein expression at 26 degrees C. Under these conditions, approximately 50% of the RAP30 remains soluble. Inclusion bodies were removed from the cell lysate by centrifugation, the supernatant was treated with polyethyleneimine at 0.5 M NaCl to remove nucleic acids, and the soluble protein was applied directly to MAb-conjugated Sepharose. After extensive washing, RAP30 was eluted with buffer containing 0. 75 M ammonium sulfate and 40% propylene glycol. RAP30 produced by this procedure stimulates transcription from a minimal promoter. This is a rapid method for purifying unmodified RAP30 without renaturing the protein from inclusion bodies.
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Affiliation(s)
- N E Thompson
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
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11
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Rossignol M, Keriel A, Staub A, Egly JM. Kinase activity and phosphorylation of the largest subunit of TFIIF transcription factor. J Biol Chem 1999; 274:22387-92. [PMID: 10428810 DOI: 10.1074/jbc.274.32.22387] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The largest subunit of the human basal transcription factor TFIIFalpha (also called RAP74) was reported previously to be the target of some phospho/dephosphorylation process. We show that TFIIFalpha possesses a serine/threonine kinase activity, allowing an autophosphorylation of the two residues at position serine 385 and threonine 389. Mutation analysis strongly suggests that autophosphorylation of both sites regulates the transcription elongation process. Moreover we also evidence three additional phosphorylation sites located at positions 207-230, 271-283, and 335-344. These sites are phosphorylated by casein kinase II-like kinases and TAF(II)250, a component of TFIID.
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Affiliation(s)
- M Rossignol
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, B. P.163, 67404 Illkirch Cedex, Communaute Urbaine de Strasbourg, France
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12
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Chédin S, Ferri ML, Peyroche G, Andrau JC, Jourdain S, Lefebvre O, Werner M, Carles C, Sentenac A. The yeast RNA polymerase III transcription machinery: a paradigm for eukaryotic gene activation. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 1999; 63:381-9. [PMID: 10384303 DOI: 10.1101/sqb.1998.63.381] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- S Chédin
- Service de Biochimie et Génétique Moléculaire, CEA/Saclay, Gif-sur-Yvette, France
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13
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Archambault J, Pan G, Dahmus GK, Cartier M, Marshall N, Zhang S, Dahmus ME, Greenblatt J. FCP1, the RAP74-interacting subunit of a human protein phosphatase that dephosphorylates the carboxyl-terminal domain of RNA polymerase IIO. J Biol Chem 1998; 273:27593-601. [PMID: 9765293 DOI: 10.1074/jbc.273.42.27593] [Citation(s) in RCA: 125] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
TFIIF (RAP30/74) is a general initiation factor that also increases the rate of elongation by RNA polymerase II. A two-hybrid screen for RAP74-interacting proteins produced cDNAs encoding FCP1a, a novel, ubiquitously expressed human protein that interacts with the carboxyl-terminal evolutionarily conserved domain of RAP74. Related cDNAs encoding FCP1b lack a carboxyl-terminal RAP74-binding domain of FCP1a. FCP1 is an essential subunit of a RAP74-stimulated phosphatase that processively dephosphorylates the carboxyl-terminal domain of the largest RNA polymerase II subunit. FCP1 is also a stoichiometric component of a human RNA polymerase II holoenzyme complex.
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Affiliation(s)
- J Archambault
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5G 1L6
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Robert F, Douziech M, Forget D, Egly JM, Greenblatt J, Burton ZF, Coulombe B. Wrapping of promoter DNA around the RNA polymerase II initiation complex induced by TFIIF. Mol Cell 1998; 2:341-51. [PMID: 9774972 PMCID: PMC4492723 DOI: 10.1016/s1097-2765(00)80278-6] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The formation of the RNA polymerase II (Pol II) initiation complex was analyzed using site-specific protein-DNA photo-cross-linking. We show that the RAP74 subunit of transcription factor (TF) IIF, through its RAP30-binding domain and an adjacent region necessary for the formation of homomeric interactions in vitro, dramatically alters the distribution of RAP30, TFIIE, and Pol II along promoter DNA between positions -40 and +26. This isomerization of the complex, which requires both TFIIF and TFIIE, is accompanied by tight wrapping of the promoter DNA for almost a full turn around Pol II. Addition of TFIIH enhances photo-cross-linking of Pol II to a number of promoter positions, suggesting that TFIIH tightens the DNA wrap around the enzyme. We present a general model to describe transcription initiation.
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Affiliation(s)
- François Robert
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, JlK 2R1, Canada
| | - Maxime Douziech
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, JlK 2R1, Canada
| | - Diane Forget
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, JlK 2R1, Canada
| | - Jean-Marc Egly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UPR 6520 (CNRS), Unité 184 (INSERM), 1 rue Laurent Fries, BP 163, Illkirch Cédex, CU de Strasbourg, France
| | - Jack Greenblatt
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Zachary F. Burton
- Department of Biochemistry, Michigan State University, East Lansing, Michigan 48824
| | - Benoit Coulombe
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, JlK 2R1, Canada
- To whom correspondence should be addressed:
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Huet J, Conesa C, Carles C, Sentenac A. A cryptic DNA binding domain at the COOH terminus of TFIIIB70 affects formation, stability, and function of preinitiation complexes. J Biol Chem 1997; 272:18341-9. [PMID: 9218475 DOI: 10.1074/jbc.272.29.18341] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
TFIIIC-dependent assembly of yeast TFIIIB on class III genes unmasks a high avidity of TFIIIB for DNA. TFIIIB contains TATA-binding protein (TBP), TFIIIB90/B", and TFIIIB70/Brf1, which is homologous to TFIIB. Using limited proteolysis, we have found that the COOH terminus of TFIIIB70 (residues 510-596) forms a protease-resistant domain that binds DNA tightly as seen by Southwestern, DNase I footprinting, and gel shift assays. Consistent with a role for this DNA binding activity, preinitiation complexes were formed less efficiently with truncated TFIIIB70 lacking the COOH-terminal domain and displayed an increased sensitivity to heparin. B' (TFIIIB70 + TBP).TFIIIC.DNA complexes were also particularly unstable. In addition, TFIIIB.TFIIIC.DNA complexes containing truncated TFIIIB70 were impaired in promoting transcription initiation.
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Affiliation(s)
- J Huet
- Service de Biochimie et Génétique Moléculaire, Commissariat à l'Energie Atomique, Saclay, F91191 Gif sur Yvette Cedex, France
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Diagana TT. [Activation of transcription in eukaryotic cells: interactions between transcription factors and components of the basal transcriptional mechanism]. COMPTES RENDUS DE L'ACADEMIE DES SCIENCES. SERIE III, SCIENCES DE LA VIE 1997; 320:509-21. [PMID: 9309252 DOI: 10.1016/s0764-4469(97)84706-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Regulation of transcription in eucaryotes is achieved by two classes of transcription factors, GTFs (general transcription factors), which are components of the basal machinery, and sequence- and tissue-specific transcription factors. In this review, recent insights into the structure and function of components from the basal transcriptional machinery are discussed. The mechanisms of transcriptional activation involving direct interactions between trans-activators and the basal machinery are also presented.
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Affiliation(s)
- T T Diagana
- Département de Biologie Moléculaire, Institut Pasteur, Paris, France
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17
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Cho H, Maldonado E, Reinberg D. Affinity purification of a human RNA polymerase II complex using monoclonal antibodies against transcription factor IIF. J Biol Chem 1997; 272:11495-502. [PMID: 9111063 DOI: 10.1074/jbc.272.17.11495] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Five different monoclonal antibodies that immunoreact with RAP74, the large subunit of general transcription factor (TF) IIF, were produced and characterized. Using one of these antibodies, an affinity purification procedure was devised to isolate a human RNA polymerase II complex. This procedure is fast, simple, and reproducible and does not require extensive purification. The RNA polymerase II complex isolated using this procedure contains SRB (suppressor of RNA polymerase B) polypeptides, transcription factors IIE and IIF, limiting amounts of TFIIH, and the TATA-binding protein, but was devoid of TFIIB.
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Affiliation(s)
- H Cho
- Howard Hughes Medical Institute, Division of Nucleic Acid Enzymology, Department of Biochemistry, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
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18
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Conaway RC, Conaway JW. General transcription factors for RNA polymerase II. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1997; 56:327-46. [PMID: 9187058 DOI: 10.1016/s0079-6603(08)61009-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- R C Conaway
- Program in Molecular and Cell Biology, Oklahoma Medical Research Foundation, Oklahoma City 73104, USA
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19
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Schnapp G, Graveley BR, Grummt I. TFIIS binds to mouse RNA polymerase I and stimulates transcript elongation and hydrolytic cleavage of nascent rRNA. MOLECULAR & GENERAL GENETICS : MGG 1996; 252:412-9. [PMID: 8879242 DOI: 10.1007/bf02173006] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Efficient transcription elongation by RNA polymerase I (Pol I) requires a specific Pol I-associated factor, termed TIF-IC. Here we show that TFIIS, a factor that has previously been shown to promote read-through past many types of blocks to elongation by RNA polymerase II, also enhances Pol I-directed transcription elongation. In a reconstituted transcription system containing purified proteins, TFIIS stimulates Pol I transcription by increasing the overall rate of RNA chain elongation. As with Pol II, ternary Pol I complexes cleave the 3' end of the nascent transcripts in response to TFIIS. The truncated RNAs remain bound to the template, are subject to pyrophosphorolysis, and can be chased into longer transcripts. Moreover, we show by immunoprecipitation and specific affinity chromatography that TFIIS physically interacts with Pol I. The results suggest that nascent transcript cleavage by TFIIS or a TFIIS-related factor may be a general mechanism by which both Pol I and Pol II can bypass transcriptional impediments.
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Affiliation(s)
- G Schnapp
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
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20
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Yamamoto RT, Nogi Y, Dodd JA, Nomura M. RRN3 gene of Saccharomyces cerevisiae encodes an essential RNA polymerase I transcription factor which interacts with the polymerase independently of DNA template. EMBO J 1996; 15:3964-73. [PMID: 8670901 PMCID: PMC452116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
RRN3 is one of the RRN genes specifically required for the transcription of rDNA by RNA polymerase I (Pol I) in Saccharomyces cerevisiae. We have cloned the gene, determined the nucleotide sequence, and found that it is an essential gene which encodes a protein of calculated molecular weight of 72 369. Extracts prepared from rrn3 mutants were defective in in vitro transcription of rDNA templates. We used extracts from a strain containing an epitope-tagged Rrn3 protein to purify a factor that could complement the mutant extracts. Using immunoaffinity purification combined with Mono Q chromatography, we obtained an essentially pure preparation of Rrn3p which complements the mutant extracts. By carrying out template commitment experiments, we found that Rrn3p is not part of the pre-initiation complex that is stable through multiple rounds of transcription. We also found that pre-incubation of Rrn3p with purified Pol I leads to stimulation of transcription upon subsequent mixing with DNA template and other transcription reaction components. Single-round transcription experiments using the detergent Sarkosyl showed that this stimulation is due to increased efficiency of formation of a Sarkosyl-resistant pre-initiation complex. Thus, Rrn3p appears to interact directly with Pol I, apparently stimulating Pol I recruitment to the promoter, and is distinct from two other Pol I-specific transcription factors, the Rrn6/7 complex and the Rrn5/9/10 complex (UAF), characterized previously.
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Affiliation(s)
- R T Yamamoto
- Department of Biological Chemistry, University of California, Irvine, CA 92717, USA
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21
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Leuther KK, Bushnell DA, Kornberg RD. Two-dimensional crystallography of TFIIB- and IIE-RNA polymerase II complexes: implications for start site selection and initiation complex formation. Cell 1996; 85:773-9. [PMID: 8646784 DOI: 10.1016/s0092-8674(00)81242-8] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
SUMMARY Transcription factors IIB (TFIIB) and IIE (TFIIE) bound to RNA polymerase II have been revealed by electron crystallography in projection at 15.7 A resolution. The results lead to simple hypotheses for the roles of these factors in the initiation of transcription. TFIIB is suggested to define the distance from TATA box to transcription start site by bringing TATA DNA in contact with polymerase at that distance from the active center of the enzyme. TFIIE is suggested to participate in a key conformational switch occurring at the active center upon polymerase-DNA interaction.
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Affiliation(s)
- K K Leuther
- Department of Structural Biology, Stanford University School of Medicine, California 94305-5400, USA
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22
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Hanada K, Song CZ, Yamamoto K, Yano K, Maeda Y, Yamaguchi K, Muramatsu M. RNA polymerase I associated factor 53 binds to the nucleolar transcription factor UBF and functions in specific rDNA transcription. EMBO J 1996; 15:2217-26. [PMID: 8641287 PMCID: PMC450146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Mouse RNA polymerase I (Pol I) has, besides its 11 bona fide subunits, three polymerase associated factors, termed PAF53, 51 and 49 with respect to the size of each molecule. In order to analyze the function of PAFs, cDNA encoding PAF53 was isolated using an oligonucleotide probe derived from an oligopeptide sequence. The cDNA of PAF53 predicts a polypeptide of 434 amino acids with a sequence similarity to yeast Pol 1 49 kDa subunit. Anti-PAF53 antibody does not block the random transcription activity of Pol I, but blocks specific transcription from mouse ribosomal RNA promoter, demonstrating the requirement of PAF53 in the accurate initiation of Pol I transcription. Moreover, PAF53 interacted with mouse UBF in vitro, as revealed by Far-Western blotting and GST pull down assays. These results, together with the accumulation of PAF53 in the nucleolus of growing cells, suggest that PAF53 is involved in the formation of the initiation complex at the promoter by mediating the interaction between Pol I and UBF for the active rRNA synthesis.
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Affiliation(s)
- K Hanada
- Department of Biochemistry, University of Tokyo School of Medicine, Japan
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23
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Ma L, Hoeijmakers JH, van der Eb AJ. Mammalian nucleotide excision repair. BIOCHIMICA ET BIOPHYSICA ACTA 1995; 1242:137-63. [PMID: 7492568 DOI: 10.1016/0304-419x(95)00008-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- L Ma
- Department of Medical Biochemistry, Leiden University, The Netherlands
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24
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Wang BQ, Burton ZF. Functional domains of human RAP74 including a masked polymerase binding domain. J Biol Chem 1995; 270:27035-44. [PMID: 7592953 DOI: 10.1074/jbc.270.45.27035] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
RAP74, the large subunit of human transcription factor IIF (TFIIF), has been analyzed by deletion mutagenesis and in vitro assays to map functional domains. Tight binding to the RAP30 subunit involves amino acids between positions 1-172. Amino acids 1-205 are minimally sufficient to stimulate accurate transcription from the adenovirus major late promoter in an extract system, although C-terminal sequences contribute to activity. A partially masked RNA polymerase II binding domain has been mapped to the C-terminal region of the protein (amino acids 363-444). Sequences near the N terminus and within the central portion of RAP74 affect accessibility of this domain. Extending this domain to 363-486 creates a peptide that binds polymerase and DNA and inhibits transcription initiation in vitro from non-promoter DNA sites. This larger C-terminal domain may modify polymerase interaction with template during initiation and/or elongation of RNA chains.
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Affiliation(s)
- B Q Wang
- Department of Biochemistry, Michigan State University, East Lansing 48824, USA
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25
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Frank DJ, Tyree CM, George CP, Kadonaga JT. Structure and function of the small subunit of TFIIF (RAP30) from Drosophila melanogaster. J Biol Chem 1995; 270:6292-7. [PMID: 7890767 DOI: 10.1074/jbc.270.11.6292] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
To study the mechanism of basal transcription by RNA polymerase II, a cDNA encoding the Drosophila homologue of the small subunit of TFIIF (also referred to as TFIIF30, RAP30, factor 5b, and gamma) was isolated. The Drosophila TFIIF30 gene is located at region 86C on the right arm of the third chromosome. The protein encoded by the cDNA, termed dTFIIF30, was synthesized in Escherichia coli and purified to greater than 95% homogeneity. In reconstituted transcription reactions with purified basal factors, the specific activity of dTFIIF30 was identical to that of its human homologue. Moreover, a carboxyl-terminal fragment, designated dF30(119-276), which contains the carboxyl-terminal 158 amino acid residues of dTFIIF30, was found to possess approximately 50% of the transcriptional activity as full-length dTFIIF30. The interaction of dTFIIF30 with the large subunit of TFIIF (also referred to as TFIIF74, RAP74, factor 5a, and beta) was investigated by glycerol gradient sedimentation analyses. In these experiments, dTFIIF30, but not dF30(119-276), assembled into a stable heteromeric complex with TFIIF74. These results, combined with those of previous work on TFIIF, support a model for TFIIF30 function in which the carboxylterminal region constitutes a functional domain that can interact with RNA polymerase II to mediate basal transcription, whereas the amino terminus comprises a domain that interacts with TFIIF74.
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Affiliation(s)
- D J Frank
- Department of Biology, University of California at San Diego, La Jolla 92093-0347
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26
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Skantar AM, Greenleaf AL. Identifying a transcription factor interaction site on RNA polymerase II. Gene Expr 1995; 5:49-69. [PMID: 7488860 PMCID: PMC6138034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/1994] [Accepted: 03/09/1995] [Indexed: 01/25/2023]
Abstract
We have generated a series of fusion proteins carrying portions of subunit IIc, the second largest subunit of Drosophila RNA polymerase I, and have used them in a domain interference assay to identify a fragment of the IIc subunit that carries the binding site for a basal transcription factor. Fusion proteins carrying a subunit IIc fragment spanning residues Ala519-Gly992 strongly inhibit promoter-driven transcription in both unfractionated nuclear extracts and in reconstituted systems. The same fusion proteins similarly inhibit dTFIIF stimulation of Pol II elongation on dC-tailed templates, suggesting that the IIc(A519-G992) fragment, which carries conserved regions D-H, interferes with transcription by binding to dTFIIF. Finally, dTFIIF can be specifically cross-linked to a GST-IIc(A519-G992) fusion protein or to subunit IIc in intact Pol II.
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Affiliation(s)
- A M Skantar
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
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27
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Chibazakura T, Kitajima S, Yonaha M, Yasukochi Y. Enhancement of bacterial transcription initiation in vitro by the 74 kDa subunit of human general transcription factor IIF (RAP74). BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1219:592-600. [PMID: 7948016 DOI: 10.1016/0167-4781(94)90217-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The human general transcription factor IIF (TFIIF) is required for an accurate transcription initiation by RNA polymerase II and shares some analogous features with the sigma subunit of bacterial RNA polymerase. As an attempt to analyze the function of TFIIF, we examined its effect on bacterial transcription in vitro. TFIIF significantly enhanced the initiation of transcription by the bacterial RNA polymerase while other general transcription factors, TATA-binding protein, TFIIB, and TFIIE, did not. The enhancement of the bacterial transcription was ascribed to the 74 kDa subunit of TFIIF (RAP74). RAP74 had an activity of enhancing the binding of the bacterial RNA polymerase to the promoter. The enhancing activity of RAP74 depended on a low molar ratio of the RNA polymerase to the template DNA. The action of RAP74 in the bacterial transcription may be related to a possible regulatory role of RAP74 in the eukaryotic transcription initiation.
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Affiliation(s)
- T Chibazakura
- Department of Molecular Genetics, Tokyo Medical and Dental University, Japan
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28
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Abstract
RNA polymerase II (Pol II) requires seven general transcription factors (GTFs) and ATP for transcription initiation. Transcription factor IIH (TFIIH) has emerged as the sole GTF with enzymatic activity. In addition to its essential role in transcription initiation, recent studies have demonstrated a direct involvement of TFIIH in DNA excision repair processes. The enzymatic properties and functional duality of TFIIH make it a prime target for regulation by viral and cellular factors.
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Affiliation(s)
- R Drapkin
- Howard Hughes Medical Institute, Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway 08854-5635
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29
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Roles for both the RAP30 and RAP74 subunits of transcription factor IIF in transcription initiation and elongation by RNA polymerase II. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(18)47303-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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30
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Chalut C, Moncollin V, Egly JM. Transcription by RNA polymerase II: a process linked to DNA repair. Bioessays 1994; 16:651-5. [PMID: 7980491 DOI: 10.1002/bies.950160910] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The proteins that are implicated in the basal transcription of protein coding genes have now been identified. Although little is known about their function, recent data demonstrate the ability of these proteins, previously called class II transcription factors, to participate in other reactions: TBP, the TATA-box binding factor, is involved in class I and III transcription, while TFIIH has been shown to possess components that are involved in the DNA repair mechanism. The involvement of some if not all of the TFIIH subunits in transcription and repair may explain the heterogeneity of the various and sometimes completely unrelated symptoms observed in xeroderma pigmentosum, Cockayne Syndrome and trichothiodystrophy disorders.
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Affiliation(s)
- C Chalut
- U184 de Biologie Moléculaire et de Génie Génétique de l'INSERM, Laboratoire de Génétique Moléculaire des Eucaryotes du CNRS, Institut de Chimie Biologique, Faculté de Médecine, Strasbourg, France
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31
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Coulombe B, Li J, Greenblatt J. Topological localization of the human transcription factors IIA, IIB, TATA box-binding protein, and RNA polymerase II-associated protein 30 on a class II promoter. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)32114-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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32
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Kephart D, Wang B, Burton Z, Price D. Functional analysis of Drosophila factor 5 (TFIIF), a general transcription factor. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)36864-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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33
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Goodrich JA, Tjian R. Transcription factors IIE and IIH and ATP hydrolysis direct promoter clearance by RNA polymerase II. Cell 1994; 77:145-56. [PMID: 8156590 DOI: 10.1016/0092-8674(94)90242-9] [Citation(s) in RCA: 279] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Using a defined RNA polymerase II (pol II) transcription system, we have investigated the roles of basal factors at discrete stages during the transcription cycle (e.g., initiation, promoter clearance, and transcript elongation). Abortive initiation assays revealed that TATA-binding protein, transcription factors TFIIB and TFIIF, and pol II were necessary and sufficient to form functional initiation complexes on both linear and supercoiled templates. By contrast, TFIIE, TFIIH, and ATP hydrolysis were additionally required during promoter clearance from linear templates, while negative supercoiling obviated the need for these auxiliary factors. Furthermore, TFIIE, TFIIH, and supercoiling were not required during elongation. Our results suggest a role for TFIIH-associated helicase activity or supercoiling during promoter clearance rather than open complex formation. These results establish abortive initiation as a useful assay for studying functional initiation complex formation in defined eukaryotic transcription systems and provide a framework for investigating regulation at different stages of the eukaryotic transcription cycle.
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Affiliation(s)
- J A Goodrich
- Department of Molecular and Cell Biology, University of California, Berkeley 94720
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34
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Ahn B, Gershon P, Moss B. RNA polymerase-associated protein Rap94 confers promoter specificity for initiating transcription of vaccinia virus early stage genes. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)37322-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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35
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Zhu H, Joliot V, Prywes R. Role of transcription factor TFIIF in serum response factor-activated transcription. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)41889-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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36
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Bakó L, Nuotio S, Dudits D, Schell J, Koncz C. RNAPII: a specific target for the cell cycle kinase complex. Results Probl Cell Differ 1994; 20:25-64. [PMID: 8036318 DOI: 10.1007/978-3-540-48037-2_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Affiliation(s)
- L Bakó
- Institute of Plant Physiology, Hungarian Academy of Sciences, Szeged
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37
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38
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Abstract
Immunoglobulin heavy chain (IgH) gene transcription in vitro can be reconstituted with a minimal reaction containing only TATA-binding protein (TBP), TFIIB, and RNA polymerase II (pol II) when the template is negatively supercoiled. Transcription from linear DNA templates containing either the IgH or the adenovirus major late promoters (MLPs) requires in addition TFIIF, TFIIE, TFIIH, and a fraction containing TFIIA and TFIIJ. Promoters vary in their activities in the minimal reaction. Initiation at the adenovirus MLP site was not observed in this reaction, even with templates containing negative superhelical density. When only TBP, TFIIB, and pol II were present in the reaction, the more negatively supercoiled the IgH template DNA was, the more active the transcription. It is suggested that the free energy of supercoiling promotes the formation of an open complex for initiation of transcription by the minimal set of transcription factors.
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Affiliation(s)
- J D Parvin
- Center for Cancer Research, Massachusetts Institute of Technology, Cambridge 02139-4307
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39
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Zawel L, Reinberg D. Initiation of transcription by RNA polymerase II: a multi-step process. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1993; 44:67-108. [PMID: 8434126 DOI: 10.1016/s0079-6603(08)60217-2] [Citation(s) in RCA: 287] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- L Zawel
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway 08854
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40
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The Basic Transcriptional Machinery. Gene Expr 1993. [DOI: 10.1007/978-1-4684-6811-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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41
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Garrett K, Serizawa H, Hanley J, Bradsher J, Tsuboi A, Arai N, Yokota T, Arai K, Conaway R, Conaway J. The carboxyl terminus of RAP30 is similar in sequence to region 4 of bacterial sigma factors and is required for function. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)35928-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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42
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Dombroski AJ, Walter WA, Record MT, Siegele DA, Gross CA. Polypeptides containing highly conserved regions of transcription initiation factor sigma 70 exhibit specificity of binding to promoter DNA. Cell 1992; 70:501-12. [PMID: 1643661 DOI: 10.1016/0092-8674(92)90174-b] [Citation(s) in RCA: 261] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The sigma 70 subunit of E. coli RNA polymerase is required for sequence-specific recognition of promoter DNA. Genetic studies and sequence analysis have indicated that sigma 70 contains two specific DNA-binding domains that recognize the two conserved portions of the prokaryotic promoter. However, intact sigma 70 does not bind to DNA. Using C-terminal and internal polypeptides of sigma 70, carrying one or both putative DNA-binding domains, we demonstrate that sigma 70 does contain two DNA-binding domains, but that N-terminal sequences inhibit the ability of intact sigma 70 to bind to DNA. Thus, we propose that sigma 70 is a sequence-specific DNA-binding protein that normally functions through an allosteric interaction with the core subunits of RNA polymerase.
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Affiliation(s)
- A J Dombroski
- Department of Bacteriology, University of Wisconsin, Madison 53706
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43
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Ham J, Steger G, Yaniv M. How do eukaryotic activator proteins stimulate the rate of transcription by RNA polymerase II? FEBS Lett 1992; 307:81-6. [PMID: 1322325 DOI: 10.1016/0014-5793(92)80906-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A large number of activator proteins have now been identified in higher and lower eukaryotes, which bind to the regulatory regions of protein-encoding genes and increase the rate at which they are transcribed by RNA polymerase II. The mechanism by which activators function is being intensively studied and some of the targets of transcriptional activation domains have now been identified. These studies have also revealed novel classes of regulatory factors, which were not anticipated by extrapolating from the principles obtained with prokaryotic promoters.
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Affiliation(s)
- J Ham
- Département des Biotechnologies, Institut Pasteur, Paris, France
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44
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Dunn J, Dunn A, Heppner D, Kim P. A discrete thyroxine-rich iodopeptide of 20,000 daltons from rabbit thyroglobulin. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)70070-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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