Pugh Lab Undergrads Present at Research Exhibition

April 17, 2019 – Pugh Lab Undergraduate Researchers, Julia Cipparulo, Matthew Driban, and Jordan John, participated in the 2019 Penn State Undergraduate Research Exhibition.


Julia Cipparulo presented her research on Developing an alternative approach to RNA-Seq

Sequencing messenger RNA provides a readout of gene expression, which is misregulated in many diseases. However, standard RNA-Seq protocols have many steps that require trained hands to perform. We are attempting to develop a simplified approach to study gene expression that uses a provided probe library and an overnight hybridization step with isolated mRNA. By streamlining sample preparation, we hope this method will be an easier, cost-effective alternative to RNA-Seq.



Abstract:Driban Presentation
The SAGA complex is a multi-functional protein complex involved in transcriptional regulation and histone modification, particularly under stress. Notably the SAGA complex has been linked to development of certain neurodegenerative diseases and cancers. To better characterize SAGA’s ability to regulate gene expression under various stressors, I analyzed SAGA’s binding characteristics under two conditions: subunit knockouts and heat shock. These analyses resulted in a clearer picture of SAGA’s regulatory role under different conditions of stress.


Jordan presented his research on Intrinsic DNA Shape features drive preferential Fis binding at its motif.

Abstract: Jordan John PresentationFis, factor for inversion stimulation, is a nucleoid-associated protein in E. coli. Here we study the binding of this protein throughout the genome. The binding of Fis is determined in part by the sequence motif, but the shape of the DNA also correlates with its binding. High occupancy Fis sites have different shape features when compared to low occupancy Fis sites despite the similar motif sequence suggesting that shape helps determine Fis binding.


Please click on either title above or pictures below to read the abstract about their research.

The New Director of EGR Training Grant!

Graduate students in the EGR training program's inaugural group.

Dr. Pugh has now been appointed as the Director of the EGR Training Grant

This NIH-sponsored Training Program prepares young scientists to excel in both experimental and computational approaches to address fundamental questions in gene regulation. Nearly all aspects of biology and human disease are rooted in gene regulation. Students in the program are vital members of the Center for Eukaryotic Gene Regulation (CEGR) community, with critical expertise in biophysics, biochemistry, molecular biology, genetics, computational biology, and statistics. Trainees are supported for a period of two years as a part of their doctoral programs.

Please click on the link to read the news story about this training grant!

Dr. Pugh Traveled to Maine

July 22 – 26, 2018- Dr. Pugh traveled to Newry, ME to attend the Gordon Research Conference on Chromatin Structure and Function. The title of Dr. Pugh’s talk was Genomic Mechanisms of Gene Regulation and Chromatin Organization.

Conference Description:

2018 Pugh – Mahony Annual Lab Outing!

Here at Pugh lab we care about building good community. That is why each year we plan various group activities outside of the lab, such as our annual lab outing. This year for our annual lab outing we camped at Ricketts Glenn, followed by an early Fourth of July barbecue. Please enjoy some picture from our outdoor adventure! Central Pennsylvania is a beautiful place to live and work!

  • Ricketts Glenn Pennsylvania

Recruiting new talent to PughLab!

We are looking for talented and motivated individuals who want to be a part of the epigenomics revolution!

We developed and use the ultra-high resolution ChIP-exo mapping technique.1 Most notably, we are using yeast and human systems to define the positional and mechanistic organization of all proteins that interact with the genome. Knowledge of protein positional organization informs of biological mechanisms that we can test using various gene editing methods.2 In human systems we look at many cell types, including clinical samples that are prepared and sequenced here in Dr. Pugh’s lab. Dr. Mahony’s lab is also investigating neuronal cells.3 What is most exciting is integrating thousands of datasets into a coherent view of genome regulation. This is what is most challenging also, as it involves developing advances in computational and statistical methods. Read more Recruiting new talent to PughLab!

How to Join the Lab

How to apply for a Postdoc Position:

  • Please send a Cover Letter, CV, and Letters of Recommendation to our Principal Investigator, Frank Pugh, at bfp2@psu.edu

How to apply to a Graduate Program:

Read more How to Join the Lab