B Franklin Pugh - Publications

Affiliations: 
Pennsylvania State University, State College, PA, United States 
Area:
Molecular Biology, Biochemistry, Microbiology Biology

70 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Aguilar-Gurrieri C, Larabi A, Vinayachandran V, Patel NA, Yen K, Reja R, Ebong IO, Schoehn G, Robinson CV, Pugh BF, Panne D. Structural evidence for Nap1-dependent H2A-H2B deposition and nucleosome assembly. The Embo Journal. PMID 27225933 DOI: 10.15252/embj.201694105  1
2016 Iwafuchi-Doi M, Donahue G, Kakumanu A, Watts JA, Mahony S, Pugh BF, Lee D, Kaestner KH, Zaret KS. The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation. Molecular Cell. 62: 79-91. PMID 27058788 DOI: 10.1016/j.molcel.2016.03.001  1
2016 Baranello L, Wojtowicz D, Cui K, Devaiah BN, Chung HJ, Chan-Salis KY, Guha R, Wilson K, Zhang X, Zhang H, Piotrowski J, Thomas CJ, Singer DS, Pugh BF, Pommier Y, et al. RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription. Cell. 165: 357-371. PMID 27058666 DOI: 10.1016/j.cell.2016.02.036  1
2016 Pugh BF, Venters BJ. Genomic Organization of Human Transcription Initiation Complexes. Plos One. 11: e0149339. PMID 26866362 DOI: 10.1371/journal.pone.0149339  1
2016 de Dieuleveult M, Yen K, Hmitou I, Depaux A, Boussouar F, Dargham DB, Jounier S, Humbertclaude H, Ribierre F, Baulard C, Farrell NP, Park B, Keime C, Carrière L, Berlivet S, ... ... Pugh BF, et al. Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells. Nature. PMID 26814966 DOI: 10.1038/nature16505  1
2015 Han GC, Vinayachandran V, Bataille AR, Park B, Chan-Salis KY, Keller CA, Long M, Mahony S, Hardison RC, Pugh BF. Genome-wide organization of GATA1 and TAL1 determined at high resolution. Molecular and Cellular Biology. PMID 26503782 DOI: 10.1128/MCB.00806-15  1
2015 Reja R, Vinayachandran V, Ghosh S, Pugh BF. Molecular mechanisms of ribosomal protein gene coregulation. Genes & Development. 29: 1942-54. PMID 26385964 DOI: 10.1101/gad.268896.115  1
2015 Schneider M, Hellerschmied D, Schubert T, Amlacher S, Vinayachandran V, Reja R, Pugh BF, Clausen T, Köhler A. The Nuclear Pore-Associated TREX-2 Complex Employs Mediator to Regulate Gene Expression. Cell. 162: 1016-28. PMID 26317468 DOI: 10.1016/j.cell.2015.07.059  0.52
2015 Wang S, Chen XA, Hu J, Jiang JK, Li Y, Chan-Salis KY, Gu Y, Chen G, Thomas C, Pugh BF, Wang Y. ATF4 Gene Network Mediates Cellular Response to the Anticancer PAD Inhibitor YW3-56 in Triple-Negative Breast Cancer Cells. Molecular Cancer Therapeutics. 14: 877-88. PMID 25612620 DOI: 10.1158/1535-7163.MCT-14-1093-T  0.52
2014 Rhee HS, Bataille AR, Zhang L, Pugh BF. Subnucleosomal structures and nucleosome asymmetry across a genome. Cell. 159: 1377-88. PMID 25480300 DOI: 10.1016/j.cell.2014.10.054  1
2014 Venters BJ, Pugh BF. Retraction: Genomic organization of human transcription initiation complexes. Nature. 513: 444. PMID 25079311 DOI: 10.1038/nature13588  1
2014 Chang GS, Chen XA, Park B, Rhee HS, Li P, Han KH, Mishra T, Chan-Salis KY, Li Y, Hardison RC, Wang Y, Pugh BF. A comprehensive and high-resolution genome-wide response of p53 to stress. Cell Reports. 8: 514-27. PMID 25043190 DOI: 10.1016/j.celrep.2014.06.030  1
2013 Venters BJ, Pugh BF. Genomic organization of human transcription initiation complexes. Nature. 502: 53-8. PMID 24048476 DOI: 10.1038/nature12535  1
2013 Yen K, Vinayachandran V, Pugh BF. SWR-C and INO80 chromatin remodelers recognize nucleosome-free regions near +1 nucleosomes. Cell. 154: 1246-56. PMID 24034248 DOI: 10.1016/j.cell.2013.08.043  0.52
2013 Li J, Liu Y, Rhee HS, Ghosh SK, Bai L, Pugh BF, Gilmour DS. Kinetic competition between elongation rate and binding of NELF controls promoter-proximal pausing. Molecular Cell. 50: 711-22. PMID 23746353 DOI: 10.1016/j.molcel.2013.05.016  1
2013 Nakahashi H, Kwon KR, Resch W, Vian L, Dose M, Stavreva D, Hakim O, Pruett N, Nelson S, Yamane A, Qian J, Dubois W, Welsh S, Phair RD, Pugh BF, et al. A genome-wide map of CTCF multivalency redefines the CTCF code. Cell Reports. 3: 1678-89. PMID 23707059 DOI: 10.1016/j.celrep.2013.04.024  1
2012 Rhee HS, Pugh BF. ChIP-exo method for identifying genomic location of DNA-binding proteins with near-single-nucleotide accuracy. Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. Unit 21.24. PMID 23026909 DOI: 10.1002/0471142727.mb2124s100  1
2012 Wal M, Pugh BF. Genome-wide mapping of nucleosome positions in yeast using high-resolution MNase ChIP-Seq. Methods in Enzymology. 513: 233-50. PMID 22929772 DOI: 10.1016/B978-0-12-391938-0.00010-0  0.32
2012 Yen K, Vinayachandran V, Batta K, Koerber RT, Pugh BF. Genome-wide nucleosome specificity and directionality of chromatin remodelers. Cell. 149: 1461-73. PMID 22726434 DOI: 10.1016/j.cell.2012.04.036  1
2012 Bryant JM, Govin J, Zhang L, Donahue G, Pugh BF, Berger SL. The linker histone plays a dual role during gametogenesis in Saccharomyces cerevisiae. Molecular and Cellular Biology. 32: 2771-83. PMID 22586276 DOI: 10.1128/MCB.00282-12  1
2012 Lee JS, Garrett AS, Yen K, Takahashi YH, Hu D, Jackson J, Seidel C, Pugh BF, Shilatifard A. Codependency of H2B monoubiquitination and nucleosome reassembly on Chd1. Genes & Development. 26: 914-9. PMID 22549955 DOI: 10.1101/gad.186841.112  0.48
2012 Chang GS, Noegel AA, Mavrich TN, Müller R, Tomsho L, Ward E, Felder M, Jiang C, Eichinger L, Glöckner G, Schuster SC, Pugh BF. Unusual combinatorial involvement of poly-A/T tracts in organizing genes and chromatin in Dictyostelium. Genome Research. 22: 1098-106. PMID 22434426 DOI: 10.1101/gr.131649.111  0.6
2012 Rhee HS, Pugh BF. Genome-wide structure and organization of eukaryotic pre-initiation complexes. Nature. 483: 295-301. PMID 22258509 DOI: 10.1038/nature10799  1
2011 Rhee HS, Pugh BF. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell. 147: 1408-19. PMID 22153082 DOI: 10.1016/j.cell.2011.11.013  1
2011 Batta K, Zhang Z, Yen K, Goffman DB, Pugh BF. Genome-wide function of H2B ubiquitylation in promoter and genic regions. Genes & Development. 25: 2254-65. PMID 22056671 DOI: 10.1101/gad.177238.111  0.96
2011 Sen P, Ghosh S, Pugh BF, Bartholomew B. A new, highly conserved domain in Swi2/Snf2 is required for SWI/SNF remodeling. Nucleic Acids Research. 39: 9155-66. PMID 21835776 DOI: 10.1093/nar/gkr622  1
2011 Zhang Z, Pugh BF. Genomic organization of H2Av containing nucleosomes in Drosophila heterochromatin. Plos One. 6: e20511. PMID 21738578 DOI: 10.1371/journal.pone.0020511  1
2011 Zhang Z, Wippo CJ, Wal M, Ward E, Korber P, Pugh BF. A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome. Science (New York, N.Y.). 332: 977-80. PMID 21596991 DOI: 10.1126/science.1200508  1
2011 Zhang L, Ma H, Pugh BF. Stable and dynamic nucleosome states during a meiotic developmental process. Genome Research. 21: 875-84. PMID 21515815 DOI: 10.1101/gr.117465.110  0.44
2011 Venters BJ, Irvin JD, Gramlich P, Pugh BF. Genome-wide transcriptional dependence on conserved regions of Mot1. Molecular and Cellular Biology. 31: 2253-61. PMID 21444714 DOI: 10.1128/MCB.01464-10  1
2011 Venters BJ, Wachi S, Mavrich TN, Andersen BE, Jena P, Sinnamon AJ, Jain P, Rolleri NS, Jiang C, Hemeryck-Walsh C, Pugh BF. A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces. Molecular Cell. 41: 480-92. PMID 21329885 DOI: 10.1016/j.molcel.2011.01.015  1
2011 Zhang Z, Pugh BF. High-resolution genome-wide mapping of the primary structure of chromatin. Cell. 144: 175-86. PMID 21241889 DOI: 10.1016/j.cell.2011.01.003  1
2011 Ghosh S, Pugh BF. Sequential recruitment of SAGA and TFIID in a genomic response to DNA damage in Saccharomyces cerevisiae. Molecular and Cellular Biology. 31: 190-202. PMID 20956559 DOI: 10.1128/MCB.00317-10  1
2010 Samorodnitsky E, Pugh BF. Genome-wide modeling of transcription preinitiation complex disassembly mechanisms using ChIP-chip data. Plos Computational Biology. 6: e1000733. PMID 20369017 DOI: 10.1371/journal.pcbi.1000733  1
2010 Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, ... ... Pugh BF, et al. Complete Khoisan and Bantu genomes from southern Africa. Nature. 463: 943-7. PMID 20164927 DOI: 10.1038/nature08795  1
2009 Jiang C, Pugh BF. A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome. Genome Biology. 10: R109. PMID 19814794 DOI: 10.1186/gb-2009-10-10-r109  0.6
2009 Koerber RT, Rhee HS, Jiang C, Pugh BF. Interaction of transcriptional regulators with specific nucleosomes across the Saccharomyces genome. Molecular Cell. 35: 889-902. PMID 19782036 DOI: 10.1016/j.molcel.2009.09.011  1
2009 Venters BJ, Pugh BF. How eukaryotic genes are transcribed. Critical Reviews in Biochemistry and Molecular Biology. 44: 117-41. PMID 19514890 DOI: 10.1080/10409230902858785  1
2009 Jiang C, Pugh BF. Nucleosome positioning and gene regulation: advances through genomics. Nature Reviews. Genetics. 10: 161-72. PMID 19204718 DOI: 10.1038/nrg2522  0.6
2009 Venters BJ, Pugh BF. A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome. Genome Research. 19: 360-71. PMID 19124666 DOI: 10.1101/gr.084970.108  1
2008 Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, Schuster SC, Albert I, Pugh BF. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Research. 18: 1073-83. PMID 18550805 DOI: 10.1101/gr.078261.108  1
2008 Yao H, Li P, Venters BJ, Zheng S, Thompson PR, Pugh BF, Wang Y. Histone Arg modifications and p53 regulate the expression of OKL38, a mediator of apoptosis. The Journal of Biological Chemistry. 283: 20060-8. PMID 18499678 DOI: 10.1074/jbc.M802940200  1
2008 Mavrich TN, Jiang C, Ioshikhes IP, Li X, Venters BJ, Zanton SJ, Tomsho LP, Qi J, Glaser RL, Schuster SC, Gilmour DS, Albert I, Pugh BF. Nucleosome organization in the Drosophila genome. Nature. 453: 358-62. PMID 18408708 DOI: 10.1038/nature06929  1
2008 Albert I, Wachi S, Jiang C, Pugh BF. GeneTrack--a genomic data processing and visualization framework. Bioinformatics (Oxford, England). 24: 1305-6. PMID 18388141 DOI: 10.1093/bioinformatics/btn119  1
2008 Lee C, Li X, Hechmer A, Eisen M, Biggin MD, Venters BJ, Jiang C, Li J, Pugh BF, Gilmour DS. NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila. Molecular and Cellular Biology. 28: 3290-300. PMID 18332113 DOI: 10.1128/MCB.02224-07  1
2007 Venters BJ, Pugh BF. Chromatin meets RNA polymerase II. Genome Biology. 8: 319. PMID 18001505 DOI: 10.1186/gb-2007-8-11-319  1
2007 Durant M, Pugh BF. NuA4-directed chromatin transactions throughout the Saccharomyces cerevisiae genome. Molecular and Cellular Biology. 27: 5327-35. PMID 17526728 DOI: 10.1128/MCB.00468-07  1
2007 Huisinga KL, Pugh BF. A TATA binding protein regulatory network that governs transcription complex assembly. Genome Biology. 8: R46. PMID 17407552 DOI: 10.1186/gb-2007-8-4-r46  0.4
2007 Albert I, Mavrich TN, Tomsho LP, Qi J, Zanton SJ, Schuster SC, Pugh BF. Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature. 446: 572-6. PMID 17392789 DOI: 10.1038/nature05632  1
2006 Ioshikhes IP, Albert I, Zanton SJ, Pugh BF. Nucleosome positions predicted through comparative genomics. Nature Genetics. 38: 1210-5. PMID 16964265 DOI: 10.1038/ng1878  1
2006 Durant M, Pugh BF. Genome-wide relationships between TAF1 and histone acetyltransferases in Saccharomyces cerevisiae. Molecular and Cellular Biology. 26: 2791-802. PMID 16537921 DOI: 10.1128/MCB.26.7.2791-2802.2006  1
2006 Irvin JD, Pugh BF. Genome-wide transcriptional dependence on TAF1 functional domains. The Journal of Biological Chemistry. 281: 6404-12. PMID 16407318 DOI: 10.1074/jbc.M513776200  1
2004 Alexander DE, Kaczorowski DJ, Jackson-Fisher AJ, Lowery DM, Zanton SJ, Pugh BF. Inhibition of TATA binding protein dimerization by RNA polymerase III transcription initiation factor Brf1. The Journal of Biological Chemistry. 279: 32401-6. PMID 15190063 DOI: 10.1074/jbc.M405782200  1
2004 Kou H, Pugh BF. Engineering dimer-stabilizing mutations in the TATA-binding protein. The Journal of Biological Chemistry. 279: 20966-73. PMID 15020592 DOI: 10.1074/jbc.M401535200  0.32
2004 Basehoar AD, Zanton SJ, Pugh BF. Identification and distinct regulation of yeast TATA box-containing genes. Cell. 116: 699-709. PMID 15006352  0.4
2004 Huisinga KL, Pugh BF. A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae. Molecular Cell. 13: 573-85. PMID 14992726  0.4
2003 Kou H, Irvin JD, Huisinga KL, Mitra M, Pugh BF. Structural and functional analysis of mutations along the crystallographic dimer interface of the yeast TATA binding protein. Molecular and Cellular Biology. 23: 3186-201. PMID 12697819 DOI: 10.1128/MCB.23.9.3186-3201.2003  1
2002 Chitikila C, Huisinga KL, Irvin JD, Basehoar AD, Pugh BF. Interplay of TBP inhibitors in global transcriptional control. Molecular Cell. 10: 871-82. PMID 12419230 DOI: 10.1016/S1097-2765(02)00683-4  1
1999 Jackson-Fisher AJ, Burma S, Portnoy M, Schneeweis LA, Coleman RA, Mitra M, Chitikila C, Pugh BF. Dimer dissociation and thermosensitivity kinetics of the Saccharomyces cerevisiae and human TATA binding proteins. Biochemistry. 38: 11340-8. PMID 10471284 DOI: 10.1021/bi990911p  0.68
1999 Jackson-Fisher AJ, Chitikila C, Mitra M, Pugh BF. A role for TBP dimerization in preventing unregulated gene expression. Molecular Cell. 3: 717-27. PMID 10394360 DOI: 10.1016/S1097-2765(01)80004-6  1
1998 Chicca JJ, Auble DT, Pugh BF. Cloning and biochemical characterization of TAF-172, a human homolog of yeast Mot1. Molecular and Cellular Biology. 18: 1701-10. PMID 9488487  1
1997 Weideman CA, Netter RC, Benjamin LR, McAllister JJ, Schmiedekamp LA, Coleman RA, Pugh BF. Dynamic interplay of TFIIA, TBP and TATA DNA. Journal of Molecular Biology. 271: 61-75. PMID 9300055 DOI: 10.1006/jmbi.1997.1152  1
1995 Jackson AJ, Ittmann M, Pugh BF. The BN51 protein is a polymerase (Pol)-specific subunit of RNA Pol III which reveals a link between Pol III transcription and pre-rRNA processing. Molecular and Cellular Biology. 15: 94-101. PMID 7799973  1
1992 Pugh BF, Tjian R. Diverse transcriptional functions of the multisubunit eukaryotic TFIID complex Journal of Biological Chemistry. 267: 679-682. PMID 1730659  1
1991 Tanese N, Pugh BF, Tjian R. Coactivators for a proline-rich activator purified from the multisubunit human TFIID complex. Genes & Development. 5: 2212-24. PMID 1748279  1
1991 Pugh BF, Tjian R. Transcription from a TATA-less promoter requires a multisubunit TFIID complex Genes and Development. 5: 1935-1945. PMID 1657708  1
1990 Peterson MG, Tanese N, Pugh BF, Tjian R. Functional domains and upstream activation properties of cloned human TATA binding protein. Science (New York, N.Y.). 248: 1625-30. PMID 2363050  1
1990 Pugh BF, Tjian R. Mechanism of transcriptional activation by Sp1: Evidence for coactivators Cell. 61: 1187-1197. PMID 2194667 DOI: 10.1016/0092-8674(90)90683-6  1
1990 Hoey T, Dynlacht BD, Peterson MG, Pugh BF, Tjian R. Isolation and characterization of the Drosophila gene encoding the TATA box binding protein, TFIID. Cell. 61: 1179-86. PMID 2194666 DOI: 10.1016/0092-8674(90)90682-5  1
1989 Pugh BF, Schutte BC, Cox MM. Extent of duplex DNA underwinding induced by RecA protein binding in the presence of ATP. Journal of Molecular Biology. 205: 487-92. PMID 2538631 DOI: 10.1016/0022-2836(89)90219-2  1
Show low-probability matches.