B. Franklin Pugh Ph.D.

Professor of Physiology and Biophysics

  • Professor of Molecular Biology and Genetics (primary appointment)

212 746 6359, 814-441-3794



Research Areas

Research Summary:

Our goal is to understand how all nuclear proteins work together to regulate genomes, and apply this knowledge towards better diagnosis and management of human diseases. We use the well-known budding yeast as both a technological and conceptual model.  To date, we have defined the positional organization along the yeast genome of nearly all mappable nuclear proteins (~500) at near single-bp resolution using the ChIP-exo assay that we developed. This provides an understanding of the structural organization of protein complexes along the genome in vivo. Assembly dynamics are next monitored through rapid reprogramming of the genome (e.g., 5 min. of acute heat shock).  Function is then assessed through CRISPR/Cas9-engineered depletion of factors, and through biochemical reconstitution of protein/DNA complexes on a genomic scale.  Parallel strategies are being conducted in model human cell lines and clinical samples. We intend to identify the mappable protein/DNA interactions that correlate best with disease states and their treatment outcomes so as to develop improved medical diagnostics.

Select Publications:

  1. Gallego LD, Schneider M, Mittal C, Polyansky AA, Romanauska A, Gudino-Carillo RM, Schubert T, Zagrovic B, Pugh, BF, Kohler, A. (2020) Liquid-liquid phase separation directs ubiquitination of gene body nucleosomes. Nature 579, 592-597. PMID: 32214243
  2. Rossi MJ, Lai WKM, Pugh BF. (2018) Simplified ChIP-exo assays. Nat Commun. 9:2842-54.  PMID: 30030442
  3. Lai, W. K. & Pugh, B. F. (2017). Genome-wide uniformity of human ‘open’ pre-initiation complexes. Genome Res 27, 15-26PMID: 27927716
  4. Rhee, H-S., Bataille, A. R., Zhang, L., and Pugh, B.F. (2014) Subnucleosomal Structures and Nucleosome Asymmetry Across a Genome. Cell 159, 1377-1388. PMID: 25480300