Franklin Pugh

Director of the Center for Eukaryotic Gene Regulation; Willaman Professor in Molecular Biology

Franklin Pugh

Research Summary

Biochemistry and genomics of eukaryotic transcription regulation.

Graduate Students

Huck Affiliations

Links

Publication Tags

Nucleosomes Chromatin Genome Genes Proteins Dna Chromatin Immunoprecipitation Yeasts Dna Binding Proteins Rna Polymerase Ii Genetic Promoter Regions Messenger Rna Ubiquitination Chromosome Mapping Histones Transcription Factor Tfiid Regulator Genes Shock Hot Temperature Phosphotransferases Histone Code Gene Expression Transcription Factors Nucleotides Saccharomyces

Most Recent Papers

Characterizing protein-DNA binding event subtypes in ChIP-exo data

Naomi Yamada, William K.M. Lai, Nina Farrell, B. Franklin Pugh, Shaun Mahony, 2019, Bioinformatics on p. 903-913

The SAGA/TREX-2 subunit Sus1 binds widely to transcribed genes and affects mRNA turnover globally

Varinia García-Molinero, José García-Martínez, Rohit Reja, Pedro Furió-Tarí, Oreto Antúnez, Vinesh Vinayachandran, Ana Conesa, B. Franklin Pugh, José E. Pérez-Ortín, Susana Rodríguez-Navarro, 2018, Epigenetics and Chromatin

Widespread and precise reprogramming of yeast protein-genome interactions in response to heat shock

Vinesh Vinayachandran, Rohit Reja, Matthew J. Rossi, Bongsoo Park, Lila Rieber, Chitvan Mittal, Shaun Mahony, B. Franklin Pugh, 2018, Genome research on p. 357-366

Genome-wide mapping of decay factor-mRNA interactions in yeast identifies nutrient-responsive transcripts as targets of the deadenylase Ccr4

Jason E. Miller, Liye Zhang, Haoyang Jiang, Yunfei Li, B. Franklin Pugh, Joseph C. Reese, 2018, G3: Genes, Genomes, Genetics on p. 315-330

Genome-wide uniformity of human 'open' pre-initiation complexes

William K.M. Lai, B. Franklin Pugh, 2017, Genome research on p. 15-26

The Histone Modification Domain of Paf1 Complex Subunit Rtf1 Directly Stimulates H2B Ubiquitylation through an Interaction with Rad6

S. Branden Van Oss, Margaret K. Shirra, Alain R. Bataille, Adam D. Wier, Kuangyu Yen, Vinesh Vinayachandran, In Ja L. Byeon, Christine E. Cucinotta, Annie Héroux, Jongcheol Jeon, Jaehoon Kim, Andrew P. VanDemark, B. Franklin Pugh, Karen M. Arndt, 2016, Molecular cell on p. 815-825

Tail and Kinase Modules Differently Regulate Core Mediator Recruitment and Function In Vivo

Célia Jeronimo, Marie France Langelier, Alain R. Bataille, John M. Pascal, B. Franklin Pugh, François Robert, 2016, Molecular cell on p. 455-466

Genomic Nucleosome Organization Reconstituted with Pure Proteins

Nils Krietenstein, Megha Wal, Shinya Watanabe, Bongsoo Park, Craig L. Peterson, Benjamin Franklin Pugh, Philipp Korber, 2016, Cell on p. 709-721.e12

Structural evidence for Nap1-dependent H2A–H2B deposition and nucleosome assembly

Carmen Aguilar-Gurrieri, Amédé Larabi, Vinesh Vinayachandran, Nisha A. Patel, Kuangyu Yen, Rohit Reja, Ima O. Ebong, Guy Schoehn, Carol V. Robinson, B. Franklin Pugh, Daniel Panne, 2016, EMBO Journal on p. 1465-1482

RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription

Laura Baranello, Damian Wojtowicz, Kairong Cui, Ballachanda N. Devaiah, Hye Jung Chung, Ka Yim Chan-Salis, Rajarshi Guha, Kelli Wilson, Xiaohu Zhang, Hongliang Zhang, Jason Piotrowski, Craig J. Thomas, Dinah S. Singer, Benjamin Franklin Pugh, Yves Pommier, Teresa M. Przytycka, Fedor Kouzine, Brian A. Lewis, Keji Zhao, David Levens, 2016, Cell on p. 357-371

Most-Cited Papers

Complete Khoisan and Bantu genomes from southern Africa

Stephan C. Schuster, Webb Miller, Aakrosh Ratan, Lynn P. Tomsho, Belinda Giardine, Lindsay R. Kasson, Robert S. Harris, Desiree C. Petersen, Fangqing Zhao, Ji Qi, Can Alkan, Jeffrey M. Kidd, Yazhou Sun, Daniela I. Drautz, Pascal Bouffard, Donna M. Muzny, Jeffrey G. Reid, Lynne V. Nazareth, Qingyu Wang, Richard Burhans, Cathy Riemer, Nicola E. Wittekindt, Priya Moorjani, Elizabeth A. Tindall, Charles G. Danko, Wee Siang Teo, Anne M. Buboltz, Zhenhai Zhang, Qianyi Ma, Arno Oosthuysen, Abraham W. Steenkamp, Hermann Oostuisen, Philippus Venter, John Gajewski, Yu Zhang, B. Franklin Pugh, Kateryna D. Makova, Anton Nekrutenko, Elaine R. Mardis, Nick Patterson, Tom H. Pringle, Francesca Chiaromonte, James C. Mullikin, Evan E. Eichler, Ross C. Hardison, Richard A. Gibbs, Timothy T. Harkins, Vanessa M. Hayes, 2010, Nature on p. 943-947

A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome

Zhenhai Zhang, Christian J. Wippo, Megha Wal, Elissa Ward, Philipp Korber, B. Franklin Pugh, 2011, Science on p. 977-980

A Comprehensive Genomic Binding Map of Gene and Chromatin Regulatory Proteins in Saccharomyces

Bryan J. Venters, Shinichiro Wachi, Travis N. Mavrich, Barbara E. Andersen, Peony Jena, Andrew J. Sinnamon, Priyanka Jain, Noah S. Rolleri, Cizhong Jiang, Christine Hemeryck-Walsh, B. Franklin Pugh, 2011, Molecular cell on p. 480-492

Genome-wide nucleosome specificity and directionality of chromatin remodelers

Kuangyu Yen, Vinesh Vinayachandran, Kiran Batta, R. Thomas Koerber, B. Franklin Pugh, 2012, Cell on p. 1461-1473

Genome-wide function of H2B ubiquitylation in promoter and genic regions

Kiran Batta, Zhenhai Zhang, Kuangyu Yen, David B. Goffman, B. Franklin Pugh, 2011, Genes and Development on p. 2254-2265

XSWR-C and INO80 chromatin remodelers recognize nucleosome-free regions near +1 nucleosomes

Kuangyu Yen, Vinesh Vinayachandran, Benjamin Franklin Pugh, 2013, Cell

High-resolution genome-wide mapping of the primary structure of chromatin

Zhenhai Zhang, B. Franklin Pugh, 2011, Cell on p. 175-186

The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation

Makiko Iwafuchi-Doi, Greg Donahue, Akshay Kakumanu, Jason A. Watts, Shaun Mahony, B. Franklin Pugh, Dolim Lee, Klaus H. Kaestner, Kenneth S. Zaret, 2016, Molecular cell on p. 79-91

ChiP-exo method for identifying genomic location of DNA-binding proteins with near-single-nucleotide accuracy

Ho Sung Rhee, B. Franklin Pugh, 2012, Current Protocols in Molecular Biology

Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells

Maud De Dieuleveult, Kuangyu Yen, Isabelle Hmitou, Arnaud Depaux, Fayçal Boussouar, Daria Bou Dargham, Sylvie Jounier, Hélène Humbertclaude, Florence Ribierre, Céline Baulard, Nina P. Farrell, Bongsoo Park, Céline Keime, Lucie Carrière, Soizick Berlivet, Marta Gut, Ivo Gut, Michel Werner, Jean François Deleuze, Robert Olaso, Jean Christophe Aude, Sophie Chantalat, Benjamin Franklin Pugh, Matthieu Gérard, 2016, Nature on p. 113-116