By: Seth Palmer
On the heels of a, professor B. Franklin Pugh and graduate student Ho Sung Rhee have published that builds on their earlier research.
Pugh and Rhee have developed a novel ultra-high resolution DNA-mapping technique called ChIP-exo — a chromatin immunoprecipitation (ChIP) assay which employs lambda exonuclease to “trim” a DNA sample to within a single base pair (bp) of a protein binding site, allowing for precise identification of the sequences bound by a given protein and thereby the genes whose transcription that protein regulates.
According to Dr. Pugh, the ChIP-exo technique yields an improvement in resolution of nearly two orders of magnitude, or one hundred fold.
Previous techniques could only trim samples to within 50-or-so bp of a binding site, at best; and as the same protein can bind to many sites — often 20-or-less bp in length — separated by thousands of bp across a genome of up to several billion bp, precise and comprehensive identification of those sites was exceedingly difficult, if not impossible, until now.
The DNA sequencing work described in these papers was performed at the Huck Institutes' Genomics Core Facility at University Park.
Dr. Pugh’s lab is part of the Huck Institutes' Center for Eukaryotic Gene Regulation.
About the researchers
B. Franklin Pugh is a Willaman Professor in Molecular Biology, a professor of biochemistry and molecular biology, and is a faculty member of the Huck Institutes' graduate programs in bioinformatics and genomics and cell and developmental biology.
Ho Sung Rhee is a graduate student in Penn State's Biochemistry and Molecular Biology program.
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