The Huck Institutes of the Life Sciences

Researchers develop new method to pinpoint and study gene-regulating proteins

B. Franklin Pugh and graduate student Ho Sung Rhee have published their results in Cell and Nature.
 
Representation of a lambda exonuclease-like protein. Image by Jawahar Swaminathan and MSD staff at the European Bioinformatics Institute, via Wikimedia Commons.

Representation of a lambda exonuclease-like protein. Image by Jawahar Swaminathan and MSD staff at the European Bioinformatics Institute, via Wikimedia Commons.

By: Seth Palmer

On the heels of a groundbreaking December publication in Cell, professor B. Franklin Pugh and graduate student Ho Sung Rhee have published another paper this month in Nature 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.

 

DNA sequencing

The DNA sequencing work described in these papers was performed at the Huck Institutes' Genomics Core Facility at University Park.

 

Pugh lab

Dr. Pugh’s lab is part of the Huck Institutes' Center for Eukaryotic Gene Regulation.

About the researchers

Dr. Pugh

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.

 

Mr. Rhee

Ho Sung Rhee is a graduate student in Penn State's Biochemistry and Molecular Biology program.

Publication details

Published:
2012
Author(s):
  • Rhee HS
  • Pugh BF
Title:
Genome-wide structure and organization of eukaryotic pre-initiation complexes
Journal:
Nature 483: 295-301
doi:
10.1038/nature10799