March 8, 2012 at 2:20 PM

As students start transitioning into spring, researchers are transitioning into a new era of gene research.

Dr. Frank Pugh, Willaman Chair in Molecular Biology, and his researchers have found a way to isolate proteins at the genes they regulate and to determine where exactly the protein bound to the gene.

Genes are the hereditary units that determine what traits, like eye and hair color, people have. They are composed of sequences of deoxyribose nucleic acid, or DNA.

These DNA sequences also are what determine which proteins bind where to control gene expression.

Pugh and his team began by isolating and purifying a particular protein using a technique called chromatin immunoprecipitation, otherwise known as ChIP. The technique uses antibodies to identify proteins associated with specific parts of a genome.

After purifying the protein they used an enzyme called exonuclease to destroy the DNA not involved in the gene they were examining, for the protein protected the DNA sequence to which it was bound.

This method, Pugh wrote in an email, reduced the noise that had interfered with previous methods, like extra DNA sequences that contaminated the samples that were being examined. He compared this noise to background noise that might interfere with someone listening to music.

These contaminations give the impression that there are additional binding sequences, Pugh wrote, and there is no way to distinguish between the actual binding sequences and the contaminations.

Once Pugh's team ran the tests, the results shocked them. They had expected the protein to bind to a few hundred places, but instead discovered that it bound to a few thousand locations - much more than they expected, even with the ChIP-exo method.

Excerpt from:
Researchers discover breakthrough with DNA testing

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