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Scientists unravel role of fusion gene in prostate cancer
Date:5/22/2012

is lab provided the expertise in computational biology and mathematical analysis needed to interpret the complex data produced by the experiments run by Dr. Rickman, his lab and members of the Rubin laboratory.

Joining them were nine other scientists from Weill Cornell Medical College, and two from Mount Sinai School of Medicine.

Dr. Elemento, Dr. Rickman and their laboratory colleagues used numerous techniques to understand the effect of the ERG oncoprotein. They first used an experimental technique called Hi-C to query chromatin interactions throughout the genome. "Chromatin interactions are inherently complex and it is easy to grasp why this is so," says Dr. Elemento. "There are about 25,000 known genes in the human genome therefore there are possibly 25,000 x 25,000 interactions between genes -- which is 625 million -- and that is only scratching the surface."

To treat the high volume of data the researchers needed to develop new statistical methods to detect chromatin interactions and the changes that occur when ERG is over-expressed.

Then, to understand why these chromatin interaction changes occurred in the first place -- what it is that ERG does to generate new interactions or abolish existing ones -- they performed additional experiments, which produced even more data. They used a technique called ChIP-seq to map where on the genome ERG likes to bind, and then used the RNA-seq tool to determine which genes are expressed or shut down when ERG is present.

More analyses were needed to identify genes and regions on the genome whose interaction patterns changed most when ERG was over-expressed. Finally, they reached what Dr. Elemento called a shocking revelation: "ERG binds very often near the genes whose interaction patterns change the most, thus indicating that ERG directly mediates the interaction by binding to these regions."

The researchers then discovered that genes whose expression was collectively inc
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Contact: Lauren Woods
law2014@med.cornell.edu
212-821-0560
New York- Presbyterian Hospital/Weill Cornell Medical Center/Weill Cornell Medical College
Source:Eurekalert

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