09 May 2014

B. Franklin Pugh, Willaman Professor in Molecular Biology and professor of biochemistry and molecular biology at Penn State University, has been honored by the University with the title of Evan Pugh Professor. The title is the highest honor that Penn State bestows on a faculty member.

Pugh has built a biochemistry research program that investigates how all genes of an organism are controlled by their environment. He uses as model systems human cells and yeast cells — both of which are among the large grouping of eukaryote cells that have a number of features in common, including a distinct nucleus. “Since the gene-transcription machinery is fundamentally the same in all eukaryotes, lessons learned from yeast provide the foundation for understanding how genes are regulated in humans, and how misregulation of genes leads to diseases such as cancer,” Pugh said. “We use yeast as a simple ‘playground’ to test ideas, then jump to human cells to see how the ideas bear out in more complex systems.”

Pugh’s research team uses the techniques of biochemistry to understand fundamental mechanisms of protein-DNA interactions. The scientists in Pugh’s lab then use genomic methods — including genome-wide location assays, genome-wide expression profiling, and bioinformatic analyses — to track the organism’s gene-transcription machinery and gene regulators as they operate throughout a genome. Pugh’s research takes advantage of cutting-edge new technologies including ‘next-generation’ DNA sequencing, which produces billions of data points.  Computational modeling of these data allows his research team to integrate related groups of biochemically-grounded regulatory mechanisms to produce a unified understanding of how complex gene-regulatory networks function. As Pugh explains, “A gene networks is akin to team of people working on different aspects of a project. Someone needs to coordinate those activities, and that is what regulatory proteins do for gene networks.” His laboratory’s work on gene regulation has resulted in more than eighty scientific papers in peer-reviewed journals.

Pugh manages an academic research laboratory with fifteen-to-twenty students, postdoctoral researchers, and technicians. One of the results of his lab’s work that is especially well known is the invention of the ChIP-exo assay, which allows the genomic binding locations of gene regulatory proteins to be identified with pinpoint accuracy. “This assay potentially allows the epigenomic landscape of any organism to be examined in detail, and this might be useful for assessing an awry epigenome in diseased cells,” Pugh said.  A patent for the process was issued in 2013. In 2012, he co-founded a company called Peconic, LLC to provide wider access to the assay.

Pugh was named a Leukemia Society of America Postdoctoral Fellow in 1988, a Searle Scholar in 1992, and a Leukemia and Lymphoma Society Scholar in 1996.  At Penn State, he was honored with a Daniel Tershak Faculty Teaching Award in 1996, a Faculty Scholar Medal in 2006, and in 2007 became holder of the Verne Willaman Chair in Molecular Biology.

He was a member of the American Cancer Society peer-review committee on Genetic Mechanisms from 1999 to 2003, and was a member of the peer-review panel for the Florida Department of Health from 2001 to 2003.  He currently is director of the Center for Eukaryotic Gene Regulation at Penn State, and Editor for the journal Molecular and Cellular Biology.

Pugh received a bachelor’s degree in biology from Cornell University in 1983 and a doctoral degree in molecular biology from the University of Wisconsin-Madison in 1987.  He was a postdoctoral research associate at the University of Wisconsin-Madison from 1987 to 1988 and at the University of California, Berkeley from 1988 to 1991.  He joined the faculty at Penn State as assistant professor of biochemistry and molecular biology in 1992.  He was promoted to associate professor in 1998 and to professor in 2005.