Technology

Pipetting

Molecular Biology

The core of CEGR research utilizes traditional and cutting edge biochemical and molecular biology methods. These include protein expression and purification systems, transcription and protein-DNA interaction assays, transgenic cells, genetics, CRISPR-Cas9, and anchor away depletions.
Imaging

Imaging

We use light microscopy, NMR, X-ray crystallography and electron microscopy imaging to visualize gene regulation molecules. [light microscopy capabilities from Lu Bai]. For examining structures of molecules and interactions that contribute to gene regulation in solution, we use high resolution NMR spectrometers, equipped with cryogenic probe technology for signal enhancement. We grow crystals of chromatin complexes in temperature controlled incubators, and examine the diffraction properties of these crystals using our in-house X-ray crystallography facility. Penn State’s recent acquisition of an FEI Titan Krios microscope with Falcon III and Gatan K2 direct electron detectors provide us with state-of-the-art single particle cryoelectron microscopy capabilities.
DNA Sequencing

DNA Sequencing

We were among the first in the world to apply deep sequencing to functional genomics. In 2007, we reported the first-ever ChIP-seq paper, which utilized the Applied Biosystems 454 sequencer to map the precise location of every nucleosome across the yeast genome. Since then we have utilized nearly every generation of deep sequencer including ABI SOLiD, and the Illumina GAII, HiSeq 2000, and NextSeq 500 series.
Bioinformatics

Bioinformatics

Many functional genomics assays are now based on deep sequencing, and thus produce vast amounts of data. Analyzing, integrating, and interpreting such data requires the development of novel computational methods. Uniquely, CEGR places computational biologists in the same laboratory space as molecular biologists. This enables close collaboration on the development of analysis methods for understanding gene regulation in high-resolution.
Cancer Epigenetics

Cancer Drug Development

The tumor suppressor p53 pathway controls important cell processes, such as cell cycle, apoptosis, and autophagy. We study epigenetic mechanisms that regulate the expression of tumor suppressor genes of the p53 pathway. In particular, we study the role of histone Arg modifications catalyzed by peptidylarginine deiminase 4 (PAD4/PADI4) in gene regulation. PAD4 is overexpressed in multiple human cancers, suggesting that PAD4 is a promising target for cancer treatment. Additionally, PAD4 is abundantly expressed in peripheral blood neutrophils. Global histone citrullination by PAD4 likely impacts on chromatin folding and unfolding in neutrophils. Our research has a broad implication to human diseases and physiology, including cancer, innate immunity, and autoimmune diseases.