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Publications by Benjamin F. Pugh

2007

Albert, I., T. N. Mavrich, L. P. Tomsho, J. Qi, S. J. Zanton, S. C. Schuster, and B. F. Pugh. Translational and rotational settings of H2A.Z nucleosomes across the S. cerevisiae genome. Nature 446:572-576.

Huisinga, K. L. and B. F. Pugh. A TATA binding protein regulatory network that governs transcription complex assembly. Genome Biol. 8:R46#.

Durant, M. and B. F. Pugh. NuA4-directed chromatin transactions throughout the S. cerevisiae genome. Mol. Cell. Biol. 15:5327-5335.

2006

Irvin, J.D. and B.F. Pugh. Genome-wide transcriptional dependence on TAF1 functional domains. J. Biol. Chem. 281:6404-6412.

Durant, M. and B.F. Pugh. Genome-wide relationships between TAF1 and histone acetyltransferases in Saccharomyces cerevisiae. Mol. Cell. Biol. 26:2791-2802.

Zanton, S.J. and B.F. Pugh. Full and partial genome-wide assembly and disassembly of the yeast transcription machinery in response to heat shock. Genes Dev. 20:2250-2265.

Ioshikhes, I., I. Albert, S.J. Zanton, and B.F. Pugh. Nucleosome positions predicted through comparative genomics. Nat. Genet. 38:1210-1215.

Pugh, B.F. HATs off to PIC assembly. Mol. Cell 23:776-777.

2004

Zanton, S.J. and B.F. Pugh. Changes in genomewide occupancy of core transcriptional regulators during heat stress. Proc. Natl. Acad. Sci. USA 101:16843-16848.

Alexander, D.E., D.J. Kaczorowski, A.J. Jackson-Fisher, D.M. Lowery, S.J. Zanton, and B.F. Pugh. Inhibition of TATA binding protein dimerization by RNA polymerase III transcription initiation factor Brf1. J. Biol. Chem. 279:32401-32406.

Kou, H. and B.F. Pugh. Engineering dimer-stabilizing mutations in the TATA-binding protein. J. Biol. Chem. 279:20966-20973.

Pugh, B.F. Is acetylation the key to opening locked gates? Nat. Struct. Mol. Biol. 11:298-300.

Basehoar, A.D., S.J. Zanton, and B.F. Pugh. Identification and distinct regulation of yeast TATA box-containing genes. Cell 116:699-709.

Huisinga, K.L. and B.F. Pugh. A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae. Mol. Cell 13:573-585.

2003

Kou, H., J.D. Irvin, K.L. Huisinga, M. Mitra, and B.F. Pugh. Structural and functional analysis of mutations along the crystallographic dimer interface of the yeast TATA binding protein. Mol. Cell. Biol. 23:3186-3201.

2002

Chitikila, C., K.L. Huisinga, J.D. Irvin, M. Mitra, and B.F. Pugh. Interplay of TBP inhibitors in global transcriptional control. Mol. Cell 10:871-882.

2001

Pugh, B.F. The RNA polymerase II transcription machinery. In: Transcription Factors. (J. Locker, ed.), pp. 1-16, BIOS Scientific Publishers, Oxford.

Pugh, B.F., and D. Gilmour. Genome-wide analysis of protein-DNA interactions in living cells. Genome Biol. 2:1013.1-1013.3.

2000

Pugh, B.F. Control of Gene Expression Through Regulation of the TATA Binding Protein. Gene 255:1-14.

1999

Coleman, R.A., A.K.P. Taggart, S. Burma, J.J. Chicca, II, and B.F. Pugh. TFIIA Regulates TBP and TFIID Dimers. Mol. Cell 4:451-457.

Jackson-Fisher, A.J., S. Burma, M. Portnoy, L. Schneeweis, R.A. Coleman, M. Mitra, C. Chitikila, and B.F. Pugh. Dimer Dissociation and Thermosensitivity Kinetics of the Saccharomyces Cerevisiae and Human TATA Binding Proteins. Biochemistry 38:11340-11348.

Jackson-Fisher, A.J., C. Chitikila, M. Mitra, and B.F. Pugh. A Role for TBP Dimerization in Preventing Unregulated Gene Expression. Mol. Cell 3:717-727.

1998

Chicca, J.J., D. Auble, and B.F. Pugh. Cloning and Biochemical Characterization of TAF-172, a Human Homologue of Yeast Mot1. Mol. Cell. Biol. 18:1701-1710.

1997

Booth, B.L. and B.F. Pugh. Identification and Characterization of a Nuclease Specific for the 3' End of the U6 Small Nuclear RNA. J. Biol. Chem. 272:984-991.

Coleman, R.A. and B.F. Pugh. Slow Dimer Dissociation of the TATA Binding Protein Dictates the Kinetics of DNA Binding. Proc. Natl. Acad. Sci. USA 94:7221-7226.

Pugh, B.F. Dynamics of Transcription Complex Assembly. In: Transcription Factors in Eukaryotes. (A.G. Papavassiliou, ed.), pp. 37-50, R.G. Landes Company Biomedical, Austin, TX.

Weideman, C.A., R.C. Netter, L.R. Benjamin, J.J. McAllister, L.A. Schmiedekamp, R.A. Coleman, and B.F. Pugh. Dynamic Interplay of TFIIA, TBP, and TATA DNA. J. Mol. Biol. 271:61-75.

1996

Taggart, A.K. and B.F. Pugh. Dimerization of TFIID When not Bound to DNA. Science 272:1331-1333.

Pugh, B.F. Mechanisms of Transcription Complex Assembly. Curr. Opin. Cell. Biol. 8:303-311.

1995

Coleman, R.A. and B.F. Pugh. Evidence for Functional Binding and Stable Sliding of the TATA Binding Protein on Nonspecific DNA. J. Biol. Chem. 270:13850-13859.

Coleman, R.A., A.K. Taggart, L.R. Benjamin, and B.F. Pugh. Dimerization of the TATA-binding Protein. J. Biol. Chem. 270:13842-13849.

Jackson, A.J., M. Ittman, and B.F. Pugh. The BN5l Protein is a Polymerase (Pol)-specific Subunit of RNA Pol III which Reveals a Link between Pol III Transcription and pre-rRNA Processing. Mol. Cell Biol. l5:94-l0l.

Pugh, B.F. Preparation of HeLa Nuclear Extracts. In: Methods in Molecular Biology, In Vitro Transcription and Translation Protocols. (M.J. Tymms, ed.), Vol. 37, pp. 349-358, Humana Press, Inc., Totowa, N.J.

Pugh, B.F. Purification of the Human TATA-binding Protein, TBP. In: Methods in Molecular Biology, In Vitro Transcription and Translation Protocols. (M.J. Tymms, ed.), Vol. 37, pp. 359-367, Humana Press, Inc., Totowa, N.J.

1992

Pugh, B.F. and R. Tjian. Review: Diverse Transcriptional Functions of the Multisubunit Eukaryotic TFIID Complex. J. Biol. Chem. 267:679-682.

Taggart, A.K.P., T.S. Fisher, and B.F. Pugh. The TATA-binding Protein and Associated Factors are Components of pol III Transcription Factor TFIIIB. Cell 71:1015-1028.

Pugh, B.F. and R. Tjian. Regulation of Transcription in Animal Cells: Factors and Mechanisms. In: Nuclear Processes and Oncogenes. (P. Sharp, ed.), pp. 201-2l0. Academic Press, Florida.

1991

Pugh, B.F. and R. Tjian. Transcription From a TATA-Less Promoter Requires the TFIID Complex. Gene Develop. 5:1935-1945.

Tanese, N., B.F. Pugh, and R. Tjian. Coactivators for a Proline-Rich Activator Purified From the Multisubunit Human TFIID Complex. Gene Develop. 5:2212-2224.


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About Us Faculty Facilities Seminars Publications News and Events Outreach Links	Publications by Benjamin F. Pugh 2007 Albert, I., T. N. Mavrich, L. P. Tomsho, J. Qi, S. J. Zanton, S. C. Schuster, and B. F. Pugh. Translational and rotational settings of H2A.Z nucleosomes across the S. cerevisiae genome. Nature 446:572-576. Huisinga, K. L. and B. F. Pugh. A TATA binding protein regulatory network that governs transcription complex assembly. Genome Biol. 8:R46#. Durant, M. and B. F. Pugh. NuA4-directed chromatin transactions throughout the S. cerevisiae genome. Mol. Cell. Biol. 15:5327-5335. 2006 Irvin, J.D. and B.F. Pugh. Genome-wide transcriptional dependence on TAF1 functional domains. J. Biol. Chem. 281:6404-6412. Durant, M. and B.F. Pugh. Genome-wide relationships between TAF1 and histone acetyltransferases in Saccharomyces cerevisiae. Mol. Cell. Biol. 26:2791-2802. Zanton, S.J. and B.F. Pugh. Full and partial genome-wide assembly and disassembly of the yeast transcription machinery in response to heat shock. Genes Dev. 20:2250-2265. Ioshikhes, I., I. Albert, S.J. Zanton, and B.F. Pugh. Nucleosome positions predicted through comparative genomics. Nat. Genet. 38:1210-1215. Pugh, B.F. HATs off to PIC assembly. Mol. Cell 23:776-777. 2004 Zanton, S.J. and B.F. Pugh. Changes in genomewide occupancy of core transcriptional regulators during heat stress. Proc. Natl. Acad. Sci. USA 101:16843-16848. Alexander, D.E., D.J. Kaczorowski, A.J. Jackson-Fisher, D.M. Lowery, S.J. Zanton, and B.F. Pugh. Inhibition of TATA binding protein dimerization by RNA polymerase III transcription initiation factor Brf1. J. Biol. Chem. 279:32401-32406. Kou, H. and B.F. Pugh. Engineering dimer-stabilizing mutations in the TATA-binding protein. J. Biol. Chem. 279:20966-20973. Pugh, B.F. Is acetylation the key to opening locked gates? Nat. Struct. Mol. Biol. 11:298-300. Basehoar, A.D., S.J. Zanton, and B.F. Pugh. Identification and distinct regulation of yeast TATA box-containing genes. Cell 116:699-709. Huisinga, K.L. and B.F. Pugh. A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae. Mol. Cell 13:573-585. 2003 Kou, H., J.D. Irvin, K.L. Huisinga, M. Mitra, and B.F. Pugh. Structural and functional analysis of mutations along the crystallographic dimer interface of the yeast TATA binding protein. Mol. Cell. Biol. 23:3186-3201. 2002 Chitikila, C., K.L. Huisinga, J.D. Irvin, M. Mitra, and B.F. Pugh. Interplay of TBP inhibitors in global transcriptional control. Mol. Cell 10:871-882. 2001 Pugh, B.F. The RNA polymerase II transcription machinery. In: Transcription Factors. (J. Locker, ed.), pp. 1-16, BIOS Scientific Publishers, Oxford. Pugh, B.F., and D. Gilmour. Genome-wide analysis of protein-DNA interactions in living cells. Genome Biol. 2:1013.1-1013.3. 2000 Pugh, B.F. Control of Gene Expression Through Regulation of the TATA Binding Protein. Gene 255:1-14. 1999 Coleman, R.A., A.K.P. Taggart, S. Burma, J.J. Chicca, II, and B.F. Pugh. TFIIA Regulates TBP and TFIID Dimers. Mol. Cell 4:451-457. Jackson-Fisher, A.J., S. Burma, M. Portnoy, L. Schneeweis, R.A. Coleman, M. Mitra, C. Chitikila, and B.F. Pugh. Dimer Dissociation and Thermosensitivity Kinetics of the Saccharomyces Cerevisiae and Human TATA Binding Proteins. Biochemistry 38:11340-11348. Jackson-Fisher, A.J., C. Chitikila, M. Mitra, and B.F. Pugh. A Role for TBP Dimerization in Preventing Unregulated Gene Expression. Mol. Cell 3:717-727. 1998 Chicca, J.J., D. Auble, and B.F. Pugh. Cloning and Biochemical Characterization of TAF-172, a Human Homologue of Yeast Mot1. Mol. Cell. Biol. 18:1701-1710. 1997 Booth, B.L. and B.F. Pugh. Identification and Characterization of a Nuclease Specific for the 3' End of the U6 Small Nuclear RNA. J. Biol. Chem. 272:984-991. Coleman, R.A. and B.F. Pugh. Slow Dimer Dissociation of the TATA Binding Protein Dictates the Kinetics of DNA Binding. Proc. Natl. Acad. Sci. USA 94:7221-7226. Pugh, B.F. Dynamics of Transcription Complex Assembly. In: Transcription Factors in Eukaryotes. (A.G. Papavassiliou, ed.), pp. 37-50, R.G. Landes Company Biomedical, Austin, TX. Weideman, C.A., R.C. Netter, L.R. Benjamin, J.J. McAllister, L.A. Schmiedekamp, R.A. Coleman, and B.F. Pugh. Dynamic Interplay of TFIIA, TBP, and TATA DNA. J. Mol. Biol. 271:61-75. 1996 Taggart, A.K. and B.F. Pugh. Dimerization of TFIID When not Bound to DNA. Science 272:1331-1333. Pugh, B.F. Mechanisms of Transcription Complex Assembly. Curr. Opin. Cell. Biol. 8:303-311. 1995 Coleman, R.A. and B.F. Pugh. Evidence for Functional Binding and Stable Sliding of the TATA Binding Protein on Nonspecific DNA. J. Biol. Chem. 270:13850-13859. Coleman, R.A., A.K. Taggart, L.R. Benjamin, and B.F. Pugh. Dimerization of the TATA-binding Protein. J. Biol. Chem. 270:13842-13849. Jackson, A.J., M. Ittman, and B.F. Pugh. The BN5l Protein is a Polymerase (Pol)-specific Subunit of RNA Pol III which Reveals a Link between Pol III Transcription and pre-rRNA Processing. Mol. Cell Biol. l5:94-l0l. Pugh, B.F. Preparation of HeLa Nuclear Extracts. In: Methods in Molecular Biology, In Vitro Transcription and Translation Protocols. (M.J. Tymms, ed.), Vol. 37, pp. 349-358, Humana Press, Inc., Totowa, N.J. Pugh, B.F. Purification of the Human TATA-binding Protein, TBP. In: Methods in Molecular Biology, In Vitro Transcription and Translation Protocols. (M.J. Tymms, ed.), Vol. 37, pp. 359-367, Humana Press, Inc., Totowa, N.J. 1992 Pugh, B.F. and R. Tjian. Review: Diverse Transcriptional Functions of the Multisubunit Eukaryotic TFIID Complex. J. Biol. Chem. 267:679-682. Taggart, A.K.P., T.S. Fisher, and B.F. Pugh. The TATA-binding Protein and Associated Factors are Components of pol III Transcription Factor TFIIIB. Cell 71:1015-1028. Pugh, B.F. and R. Tjian. Regulation of Transcription in Animal Cells: Factors and Mechanisms. In: Nuclear Processes and Oncogenes. (P. Sharp, ed.), pp. 201-2l0. Academic Press, Florida. 1991 Pugh, B.F. and R. Tjian. Transcription From a TATA-Less Promoter Requires the TFIID Complex. Gene Develop. 5:1935-1945. Tanese, N., B.F. Pugh, and R. Tjian. Coactivators for a Proline-Rich Activator Purified From the Multisubunit Human TFIID Complex. Gene Develop. 5:2212-2224.
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