Vanderbilt University School of Medicine

Weil, P. Anthony , Ph.D.
Professor of Molecular Physiology and Biophysics

Lab Url:

Phone Number: 615-322-7007


Weil, P.'s picture

Office Address   Mailing Address

746A Robinson Research Building

746A Robinson Research Building 21st and Garland 37232-0615

Research Keywords
Eukaryotic Transcription, Gene Expression, Transcription Initiation, RNA Polymerase, TFIID, TFIIIB, Mot1p ,Biochemistry,Chromatin,Gene regulation,Genetics,Mass spectroscopy,Proteomics,Spectroscopy,Transcription,Transcription factor,Yeast

Research Specialty
Molecular mechanisms of transcriptional regulation

Research Description
The focus of research in our laboratory is to understand the molecular mechanisms of eukaryotic transcription initiation. For the last ten or so years we have been examining the eukaryotic transcription factors which mediate initiation complex formation and thus represent potential targets for trans-regulation. We have utilized the simple eukaryote, Saccharomyces cerevisiae or Baker's Yeast, for our work. This organism was chosen for our studies because both biochemical and genetic approaches can be taken with yeasts. In our experiments we study the factors required for transcription initiation by RNA polymerase II (RNAP II). RNAP II transcribes the genes which encode mRNAs. We have developed methods for the solubilization, characterization and purification of the complete complement of RNAP II-specific factors, and our current focus is on one of these factors the multisubunit factor termed TFIID. All of the proteins which comprise TFIID have very interesting biochemical properties. One of the factors, known as TBP, or TATA box Binding Protein, is a sequence specific DNA binding protein which interacts with the ubiquitous TATA box promoter element. while others are not. The other subunits of TFIID presumably interact with other promoter elements, RNAPII, positive-acting transcription factors or other general transcription factors such as TFIIA, TFIIB, TFIIE, TFIIF or TFIIF.

Our immediate efforts have been expended towards cloning the yeast genes which encode these genes encoding the TFIID subunits. We have been successful in cloning the genes which encode the multiple (15 distinct genes) subunits of yeast TFIID. Our interest in cloning these genes are several and are summarized here as are the types of studies which will be the focus of our research in the future--each could comprise a student rotation project: 1) The cloned genes give us the wherewithal to overexpress the corresponding gene products. Purified factors prepared from the cloned genes will be used for in vitro mechanistic studies. 2) Using the cloned genes we are examining the structure-function relationships of these important molecules. 3) We are dissecting the genetic control elements which regulate expression of the transcription factor genes themselves. These studies are being performed with an eye towards understanding global control of macromolecular biosynthesis. 4) Finally, we are using the cloned genes, in conditionally lethal forms, to identify via suppressor analyses genes whose products interact with these multi-functional general transcription initiation factors. Specific examples of the types of studies and the results which we have obtained are listed in "Selected Publications."

Arnett, DR, Jennings, JL, Tabb, DL, Link, AJ, Weil, PA. A proteomic analysis of yeast Mot1p protein-protein associations: insights into mechanism. Mol Cell Proteomics, , , 2008. PMCID:2577210

Bendjennat, M, Weil, PA. The transcriptional repressor activator protein Rap1p is a direct regulator of TATA-binding protein. J Biol Chem, 283(13), 8699-710, 2008. PMCID:2417159

Garbett, KA, Tripathi, MK, Cencki, B, Layer, JH, Weil, PA. Yeast TFIID serves as a coactivator for Rap1p by direct protein-protein interaction. Mol Cell Biol, 27(1), 297-311, 2007. PMCID:1800639

Leurent, Claire, Sanders, Steven L, Dem??ny, M? t?? A, Garbett, Krassimira A, Ruhlmann, Christine, Weil, P Anthony, Tora, L? szl??, Schultz, Patrick. Mapping key functional sites within yeast TFIID. EMBO J, 23(4), 719-27, 2004. PMCID:381015

Powell, David W, Weaver, Connie M, Jennings, Jennifer L, McAfee, K Jill, He, Yue, Weil, P Anthony, Link, Andrew J. Cluster analysis of mass spectrometry data reveals a novel component of SAGA. Mol Cell Biol, 24(16), 7249-59, 2004. PMCID:479721

Singh, Madhu V, Bland, Christin E, Weil, P Anthony. Molecular and genetic characterization of a Taf1p domain essential for yeast TFIID assembly. Mol Cell Biol, 24(11), 4929-42, 2004. PMCID:416396

Gumbs, Orlando H., Campbell, Allyson M., Weil, P.Anthony. High-affinity DNA binding by a Mot1p-TBP complex: implications for TAF-independent transcription. EMBO J, 22, 3131-3141, 2003. PMCID:162156

Klein, Joachim, Nolden, Mark, Sanders, Steven L, Kirchner, Jay, Weil, P Anthony, Melcher, Karsten, . Use of a genetically introduced cross-linker to identify interaction sites of acidic activators within native transcription factor IID and SAGA.. J Biol Chem, 278, 6779-86, 2003.

Andrau, Jean-Christophe, Van Oevelen, Chris J C, Van Teeffelen, Hetty A A M, Weil, P Anthony, Holstege, Frank C P, Timmers, H Th Marc, . Mot1p is essential for TBP recruitment to selected promoters during in vivo gene activation.. EMBO J, 21, 5173-83, 2002. PMCID:129025

Kirschner, Doris B, vom Baur, Elmar, Thibault, Christelle, Sanders, Steven L, Gangloff, Yann-Ga? PMCID:133751

Leurent, Claire, Sanders, Steven, Ruhlmann, Christine, Mallouh, V??ronique, Weil, P Anthony, Kirschner, Doris B, Tora, Laszlo, Schultz, Patrick, . Mapping histone fold TAFs within yeast TFIID.. EMBO J, 21, 3424-33, 2002. PMCID:126091

Sanders, Steven L, Garbett, Krassimira A, Weil, P Anthony. Molecular characterization of Saccharomyces cerevisiae TFIID. Mol Cell Biol, 22, 6000-13, 2002. PMCID:133964

Sanders, Steven L, Jennings, Jennifer, Canutescu, Adrian, Link, Andrew J, Weil, P Anthony. Proteomics of the eukaryotic transcription machinery: identification of proteins associated with components of yeast TFIID by multidimensional mass spectrometry. Mol Cell Biol, 22, 4723-38, 2002. PMCID:133885

Singh, Madhu V, Weil, P Anthony. A method for plasmid purification directly from yeast. Anal Biochem, 307(1), 13-7, 2002.

Thuault, Sylvie, Gangloff, Yann-Ga?

Banik, U, Beechem, J M, Klebanow, E, Schroeder, S, Weil, P A. Fluorescence-based analyses of the effects of full-length recombinant TAF130p on the interaction of TATA box-binding protein with TATA box DNA. J Biol Chem, 276, 49100-9, 2001.

Gangloff, Y G, Sanders, S L, Romier, C, Kirschner, D, Weil, P A, Tora, L, Davidson, I. Histone folds mediate selective heterodimerization of yeast TAF(II)25 with TFIID components yTAF(II)47 and yTAF(II)65 and with SAGA component ySPT7. Mol Cell Biol, 21(5), 1841-53, 2001. PMCID:86751

Kirchner, J, Sanders, S L, Klebanow, E, Weil, P A. Molecular genetic dissection of TAF25, an essential yeast gene encoding a subunit shared by TFIID and SAGA multiprotein transcription factors. Mol Cell Biol, 21, 6668-80, 2001. PMCID:99812

Sanders, S L, Weil, P A. Identification of two novel TAF subunits of the yeast Saccharomyces cerevisiae TFIID complex. J Biol Chem, 275(18), 13895-900, 2000.

Sanders, S., Klebanow, E. and P. A. Weil (1999) TAF25p, A Non-Histone-Like Subunit of TFIID and SAGA Complexes, is Essential for Total mRNA Gene Transcription In Vivo, J. Biol. Chem. 274:18847-18851.

Klebanow, E R, Weil, P A. A rapid technique for the determination of unknown plasmid library insert DNA sequence directly from intact yeast cells. Yeast, 15(6), 527-31, 1999.

Muldrow, T A, Campbell, A M, Weil, P A, Auble, D T. MOT1 can activate basal transcription in vitro by regulating the distribution of TATA binding protein between promoter and nonpromoter sites. Mol Cell Biol, 19(4), 2835-45, 1999. PMCID:84076

Reuter, T.A., Campbell, A.M., Weil P.A. and Auble, D.T. Mot1p Can Activate Basal Transcription In Vitro by Regulating the Distribution of TBP Between Promoter and Nonpromoter Sites. Mol. and Cellular Biology, 19, 2835-2845, 1999.

Sanders, S L, Klebanow, E R, Weil, P A. TAF25p, a non-histone-like subunit of TFIID and SAGA complexes, is essential for total mRNA gene transcription in vivo. J Biol Chem, 274(27), 18847-50, 1999.

Schroeder, S. and Weil, P.A. (1998) Biochemical and Genetic Characterization of the Dominant Positive Element Driving Transcription of the Yeast TBP-encoding Gene, SPT15, Nucleic Acids Research 26:4185-4196.

Drysdale, C M, Jackson, B M, McVeigh, R, Klebanow, E R, Bai, Y, Kokubo, T, Swanson, M, Nakatani, Y, Weil, P A, Hinnebusch, A G. The Gcn4p activation domain interacts specifically in vitro with RNA polymerase II holoenzyme, TFIID, and the Adap-Gcn5p coactivator complex. Mol Cell Biol, 18(3), 1711-24, 1998. PMCID:108886

Komarnitsky, P B, Klebanow, E R, Weil, P A, Denis, C L. ADR1-mediated transcriptional activation requires the presence of an intact TFIID complex. Mol Cell Biol, 18(10), 5861-7, 1998. PMCID:109172

Patterson, G H, Schroeder, S C, Bai, Y, Weil, A, Piston, D W. Quantitative imaging of TATA-binding protein in living yeast cells. Yeast, 14(9), 813-25, 1998.

Patterson, G.H., Schroeder, S.C., Bai, Y., P. A. Weil and David W. Piston . Quantitative Imaging of Green Fluorescent Protein-TBP fusion Proteins: Asymmetric Distribution of TBP between Yeast Mothers and Daughters. Yeast, 14, 813-825, 1998.

Schroeder, S C, Weil, P A. Genetic tests of the role of Abf1p in driving transcription of the yeast TATA box bindng protein-encoding gene, SPT15. J Biol Chem, 273(31), 19884-91, 1998.

Schroeder, S C, Weil, P A. Biochemical and genetic characterization of the dominant positive element driving transcription ofthe yeast TBP-encoding gene, SPT15. Nucleic Acids Res, 26(18), 4186-95, 1998. PMCID:147844

Schroeder, S. and Weil, P.A. Genetic Tests of the Role of Abf1p in Driving Transcription of the Yeast TBP- encoding Gene. J. Biol. Chem., 273, 19884-19891, 1998.

Bai, Y, Perez, G M, Beechem, J M, Weil, P A. Structure-function analysis of TAF130: identification and characterization of a high-affinity TATA-binding protein interaction domain in the N terminus of yeast TAF(II)130. Mol Cell Biol, 17(6), 3081-93, 1997. PMCID:232161

Bai, Y. , Perez, G.M., Beechem, J.M. and Weil, P.A. Structure-Function Analysis of TAF130: Identification and Characterization of a High Affinity TBP Interaction Domain in the N-terminus of yTAFII130. Molecular and Cellular Biology, 17, 3081-3093, 1997.

Klebanow, E R, Poon, D, Zhou, S, Weil, P A. Cloning and characterization of an essential Saccharomyces cerevisiae gene, TAF40, which encodes yTAFII40, an RNA polymerase II-specific TATA-binding protein-associated factor. J Biol Chem, 272(14), 9436-42, 1997.

Yamamoto, T, Poon, D, Weil, P A, Horikoshi, M. Molecular genetic elucidation of the tripartite structure of the Schizosaccharomyces pombe 72 kDa TFIID subunit which contains a WD40 structural motif. Genes Cells, 2(4), 245-54, 1997.

Klebanow, E R, Poon, D, Zhou, S, Weil, P A. Isolation and characterization of TAF25, an essential yeast gene that encodes an RNA polymerase II-specific TATA-binding protein-associated factor. J Biol Chem, 271(23), 13706-15, 1996.

Moqtaderi, Z, Bai, Y, Poon, D, Weil, P A, Struhl, K. TBP-associated factors are not generally required for transcriptional activation in yeast. Nature, 383(6596), 188-91, 1996.

Moqtaderi, Z., Bai, Y., Poon, D., Weil, P.A. and Struhl, K. TBP-associated factors are not generally required for transcriptional activation in yeast. Nature, 383, 188-191, 1996.

Perez-Howard, G M, Weil, P A, Beechem, J M. Yeast TATA binding protein interaction with DNA: fluorescence determination of oligomeric state, equilibrium binding, on-rate, and dissociation kinetics. Biochemistry, 34(25), 8005-17, 1995.

Poon, D, Bai, Y, Campbell, A M, Bjorklund, S, Kim, Y J, Zhou, S, Kornberg, R D, Weil, P A. Identification and characterization of a TFIID-like multiprotein complex from Saccharomyces cerevisiae. Proc Natl Acad Sci U S A, 92(18), 8224-8, 1995. PMCID:41129

Henry, N L, Campbell, A M, Feaver, W J, Poon, D, Weil, P A, Kornberg, R D. TFIIF-TAF-RNA polymerase II connection. Genes Dev, 8(23), 2868-78, 1994.

Leibham, D, Wong, M W, Cheng, T C, Schroeder, S, Weil, P A, Olson, E N, Perry, M. Binding of TFIID and MEF2 to the TATA element activates transcription of the Xenopus MyoDa promoter. Mol Cell Biol, 14(1), 686-99, 1994. PMCID:358418

Poon, D, Campbell, A M, Bai, Y, Weil, P A. Yeast Taf170 is encoded by MOT1 and exists in a TATA box-binding protein (TBP)-TBP-associated factor complex distinct from transcription factor IID. J Biol Chem, 269(37), 23135-40, 1994.

Robinson, G L, Cordle, S R, Henderson, E, Weil, P A, Teitelman, G, Stein, R. Isolation and characterization of a novel transcription factor that binds to and activates insulin control element-mediated expression. Mol Cell Biol, 14(10), 6704-14, 1994. PMCID:359201

Schroeder, S C, Wang, C K, Weil, P A. Identification of the cis-acting DNA sequence elements regulating the transcription of the Saccharomyces cerevisiae gene encoding TBP, the TATA box binding protein. J Biol Chem, 269(45), 28335-46, 1994.

Poon, D, Knittle, R A, Sabelko, K A, Yamamoto, T, Horikoshi, M, Roeder, R G, Weil, P A. Genetic and biochemical analyses of yeast TATA-binding protein mutants. J Biol Chem, 268(7), 5005-13, 1993.

Poon, D, Weil, P A. Immunopurification of yeast TATA-binding protein and associated factors. Presence of transcription factor IIIB transcriptional activity. J Biol Chem, 268(21), 15325-8, 1993.

Parsons, M C, Weil, P A. Cloning of TFC1, the Saccharomyces cerevisiae gene encoding the 95-kDa subunit of transcription factor TFIIIC. J Biol Chem, 267(5), 2894-901, 1992.

Yamamoto, T, Horikoshi, M, Wang, J, Hasegawa, S, Weil, P A, Roeder, R G. A bipartite DNA binding domain composed of direct repeats in the TATA box binding factor TFIID. Proc Natl Acad Sci U S A, 89(7), 2844-8, 1992. PMCID:48759

Cordle, S R, Henderson, E, Masuoka, H, Weil, P A, Stein, R. Pancreatic beta-cell-type-specific transcription of the insulin gene is mediated by basic helix-loop-helix DNA-binding proteins. Mol Cell Biol, 11(3), 1734-8, 1991. PMCID:369485

Cordle, S R, Whelan, J, Henderson, E, Masuoka, H, Weil, P A, Stein, R. Insulin gene expression in nonexpressing cells appears to be regulated by multiple distinct negative-acting control elements. Mol Cell Biol, 11(5), 2881-6, 1991. PMCID:360077

Poon, D, Schroeder, S, Wang, C K, Yamamoto, T, Horikoshi, M, Roeder, R G, Weil, P A. The conserved carboxy-terminal domain of Saccharomyces cerevisiae TFIID is sufficient to support normal cell growth. Mol Cell Biol, 11(10), 4809-21, 1991. PMCID:361446

Felts, S J, Weil, P A, Chalkley, R. Transcription factor requirements for in vitro formation of transcriptionally competent 5S rRNA gene chromatin. Mol Cell Biol, 10(5), 2390-401, 1990. PMCID:360587

Hoffmann, A, Horikoshi, M, Wang, C K, Schroeder, S, Weil, P A, Roeder, R G. Cloning of the Schizosaccharomyces pombe TFIID gene reveals a strong conservation of functional domains present in Saccharomyces cerevisiae TFIID. Genes Dev, 4(7), 1141-8, 1990.

Horikoshi, M, Yamamoto, T, Ohkuma, Y, Weil, P A, Roeder, R G. Analysis of structure-function relationships of yeast TATA box binding factor TFIID. Cell, 61(7), 1171-8, 1990.

Karnitz, L, Poon, D, Weil, P A, Chalkley, R. Identification and purification of a yeast transcriptional trans-activator. The yeast homolog of the Rous sarcoma virus internal enhancer binding factor. J Biol Chem, 265(11), 6131-8, 1990.

Parsons, M C, Weil, P A. Purification and characterization of Saccharomyces cerevisiae transcription factor TFIIIC. Polypeptide composition defined with polyclonal antibodies. J Biol Chem, 265(9), 5095-103, 1990.

Whelan, J, Cordle, S R, Henderson, E, Weil, P A, Stein, R. Identification of a pancreatic beta-cell insulin gene transcription factor that binds to and appears to activate cell-type-specific expression: its possible relationship to other cellular factors that bind to a common insulin gene sequence. Mol Cell Biol, 10(4), 1564-72, 1990. PMCID:362261

Horikoshi, M, Wang, C K, Fujii, H, Cromlish, J A, Weil, P A, Roeder, R G. Cloning and structure of a yeast gene encoding a general transcription initiation factor TFIID that binds to the TATA box. Nature, 341(6240), 299-303, 1989.

Horikoshi, M, Wang, C K, Fujii, H, Cromlish, J A, Weil, P A, Roeder, R G. Purification of a yeast TATA box-binding protein that exhibits human transcription factor IID activity. Proc Natl Acad Sci U S A, 86(13), 4843-7, 1989. PMCID:297511

Karnitz, L, Poon, D, Weil, P A, Chalkley, R. Purification and properties of the Rous sarcoma virus internal enhancer binding factor. Mol Cell Biol, 9(5), 1929-39, 1989. PMCID:362984

Nichols, M, Bell, J, Klekamp, M S, Weil, P A, S??ll, D. Multiple mutations of the first gene of a dimeric tRNA gene abolish in vitro tRNA gene transcription. J Biol Chem, 264(29), 17084-90, 1989.

Wang, C K, Weil, P A. Purification and characterization of Saccharomyces cerevisiae transcription factor IIIA. J Biol Chem, 264(2), 1092-9, 1989.

Whelan, J, Poon, D, Weil, P A, Stein, R. Pancreatic beta-cell-type-specific expression of the rat insulin II gene is controlled by positive and negative cellular transcriptional elements. Mol Cell Biol, 9(8), 3253-9, 1989. PMCID:362369

Felts, S J, Weil, P A, Chalkley, R. Novobiocin inhibits interactions required for yeast TFIIIB sequestration during stable transcription complex formation in vitro. Nucleic Acids Res, 15(4), 1493-506, 1987. PMCID:340563

Klekamp, M S, Weil, P A. Properties of yeast class III gene transcription factor TFIIIB. Implications regarding mechanism of action. J Biol Chem, 262(16), 7878-83, 1987.

Klekamp, M S, Weil, P A. Partial purification and characterization of the Saccharomyces cerevisiae transcription factor TFIIIB. J Biol Chem, 261(6), 2819-27, 1986.

Klekamp, M S, Weil, P A. Yeast class III gene transcription factors and homologous RNA polymerase III form ternary transcription complexes stable to disruption by N-lauroyl-sarcosine (sarcosyl). Arch Biochem Biophys, 246(2), 783-800, 1986.

Klekamp, M S, Weil, P A. Specific transcription of homologous class III genes in yeast-soluble cell-free extracts. J Biol Chem, 257(14), 8432-41, 1982.

Matsui, T, Segall, J, Weil, P A, Roeder, R G. Multiple factors required for accurate initiation of transcription by purified RNA polymerase II. J Biol Chem, 255(24), 11992-6, 1980.

Weil, P A, Luse, D S, Segall, J, Roeder, R G. Selective and accurate initiation of transcription at the Ad2 major late promotor in a soluble system dependent on purified RNA polymerase II and DNA. Cell, 18(2), 469-84, 1979.

Weil, P A, Segall, J, Harris, B, Ng, S Y, Roeder, R G. Faithful transcription of eukaryotic genes by RNA polymerase III in systems reconstituted with purified DNA templates. J Biol Chem, 254(13), 6163-73, 1979.

Weil, P A, Sidikaro, J, Stancel, G M, Blatti, S P. Hormonal control of transcription in the rat uterus. Stimulation of deoxyribonucleic acid-dependent RNA polymerase III by estradiol. J Biol Chem, 252(3), 1092-8, 1977.

Weil, P A, Blatti, S P. HeLa cell deoxyribonucleic acid dependent RNA polymerases: function and properties of the class III enzymes. Biochemistry, 15(7), 1500-9, 1976.

Weil, P A, Blatti, S P. Partial purification and properties of calf thymus deoxyribonucleic acid dependent RNA polymerase III. Biochemistry, 14(8), 1636-42, 1975.

Weil, P A, Hampel, A. Preparative agarose gel electrophoresis of ribonucleic acid. Biochemistry, 12(22), 4361-7, 1973.

Postdoctoral Position Available

Postdoctoral Position Details

Two postdoctoral positions available to examine the role of TBP, the TATA box Binding Protein and its associated protein factors in RNA Polymerase II-mediated transcription initiation using the Bakers yeast Saccharomyces cerevisiae system. We currently utilize a combination of biochemical, genetic, biophysical and proteomics methods to study the regulation and interactions of these proteins with each other, DNA and other transcription factors; details can be obtained at: parties should send a CV and names of references to: Dr. Tony Weil, Department of Molecular Physiology & Biophysics, Vanderbilt University, School of Medicine, Nashville, TN 37232-0615. Phone: 615-322-7007, FAX: 615-322-7236; Email:

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