P. Anthony Weil, Ph.D.
Professor of Molecular Physiology & Biophysics
Vanderbilt University Medical Center
746 Robinson Research Building
Nashville, TN 37232-0615
Molecular mechanisms of transcriptional regulation
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.
- 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.
- 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.
- 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.
- Leurent, Claire, Sanders, Steven L, DemÃ©ny, MÃ tÃ© A, Garbett, Krassimira A, Ruhlmann, Christine, Weil, P Anthony, Tora, LÃ szlÃ², Schultz, Patrick Mapping key functional sites within yeast TFIID. EMBO J, 23(4), 719-27, 2004.
- 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.
- 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, 223131-3141, 2003.
- 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, 2786779-86, 2003.
- Singh, Madhu V, Weil, P Anthony A method for plasmid purification directly from yeast. Anal Biochem, 307(1), 13-7, 2002.
- Kirschner, Doris B, vom Baur, Elmar, Thibault, Christelle, Sanders, Steven L, Gangloff, Yann-GaÃ«l, Davidson, Irwin, Weil, P Anthony, Tora, LÃ szlÃ² Distinct mutations in yeast TAF(II)25 differentially affect the composition of TFIID and SAGA complexes as well as global gene expression patterns. Mol Cell Biol, 22(9), 3178-93, 2002.
- Thuault, Sylvie, Gangloff, Yann-GaÃ«l, Kirchner, Jay, Sanders, Steven, Werten, Sebastiaan, Romier, Christophe, Weil, P Anthony, Davidson, Irwin, Functional analysis of the TFIID-specific yeast TAF4 (yTAF(II)48) reveals an unexpected organization of its histone-fold domain.. J Biol Chem, 27745510-7, 2002.
- Leurent, Claire, Sanders, Steven, Ruhlmann, Christine, Mallouh, VÃ©ronique, Weil, P Anthony, Kirschner, Doris B, Tora, Laszlo, Schultz, Patrick, Mapping histone fold TAFs within yeast TFIID.. EMBO J, 213424-33, 2002.
- Sanders, Steven L, Garbett, Krassimira A, Weil, P Anthony Molecular characterization of Saccharomyces cerevisiae TFIID. Mol Cell Biol, 226000-13, 2002.
- 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, 215173-83, 2002.
- 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, 224723-38, 2002.
- 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, 27649100-9, 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.
- 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, 216668-80, 2001.
- 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.
- 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, 192835-2845, 1999.
- 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.
- 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.
- 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.
- 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.
- 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., 27319884-19891, 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.
- 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, 14813-825, 1998.
- 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.
- 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.
- 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.
- 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, 173081-3093, 1997.
- 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.
- 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. and Struhl, K "TBP-associated factors are not generally required for transcriptional activation in yeast." Nature, 383188-191, 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Nichols, M, Bell, J, Klekamp, M S, Weil, P A, SÃ¶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.
- 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.
- Wang, C K, Weil, P A Purification and characterization of Saccharomyces cerevisiae transcription factor IIIA. J Biol Chem, 264(2), 1092-9, 1989.
- 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.
- 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.
- 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.
- 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, 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, 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, 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.