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


Publication Tags

Genome Genes Nucleosomes Chromatin Proteins Dna Histones Nucleotides Dna Binding Proteins Chromatin Immunoprecipitation Yeasts Ubiquitination Genetic Promoter Regions Exonucleases Messenger Rna Transcription Factors Transcription Factor Tfiid Histone Code Assays Noise Liver Chromosome Mapping Rna Stability Catabolite Repression Constitutive Androstane Receptor

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

Simplified ChIP-exo assays

Matthew Rossi, William Lai, Benjamin Franklin Pugh, 2018, Nature communications

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

2018, Bioinformatics

Genome-wide determinants of sequence-specific DNA binding of general regulatory factors

Matthew Rossi, William Lai, Benjamin Franklin Pugh, 2018, Genome research on p. 497-508

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

In vivo genome-wide binding interactions of mouse and human constitutive androstane receptors reveal novel gene targets

Ben Niu, Denise M. Coslo, Alain R. Bataille, Istvan Albert, Benjamin Franklin Pugh, Curtis John Omiecinski, 2018, Nucleic acids research on p. 8385-8403

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

Correspondence: DNA shape is insufficient to explain binding.

Matthew Rossi, Lai WKM, Benjamin Pugh, 2017, Nature communications on p. 15643

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

Most-Cited Papers

Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution

Ho Sung Rhee, Benjamin Franklin Pugh, 2011, Cell on p. 1408-1419

Genome-wide structure and organization of eukaryotic pre-initiation complexes

Ho Sung Rhee, Benjamin Franklin Pugh, 2012, Nature on p. 295-301

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

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

A Genome-wide Map of CTCF Multivalency Redefines the CTCF Code

Hirotaka Nakahashi, Kyong Rim Kieffer Kwon, Wolfgang Resch, Laura Vian, Marei Dose, Diana Stavreva, Ofir Hakim, Nathanael Pruett, Steevenson Nelson, Arito Yamane, Jason Qian, Wendy Dubois, Scott Welsh, Robert D. Phair, B. Franklin Pugh, Victor Lobanenkov, Gordon L. Hager, Rafael Casellas, 2013, Cell Reports on p. 1678-1689

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

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

Subnucleosomal structures and nucleosome asymmetry across a genome

Ho Sung Rhee, Alain R. Bataille, Liye Zhang, B. Franklin Pugh, 2014, Cell on p. 1377-1388

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