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The study of cancer epigenetics indicates that “gene-silencing” proteins play a role in the disease by stably turning off genes inside the cell nucleus. Now, researchers from Rice University and Baylor College of Medicine in Houston, Texas, have found a way to speed research in the field by rapidly identifying those genes that proteins can target for silencing.

Their study uses a new computer program called EpiPredictor to search any genome to identify specific genes affected by epigenetic proteins. Lead investigator Jianpeng Ma, PhD, professor of bioengineering at Rice University, describes the new field of cancer epigenetics as a board game for which scientists know some of the rules and a few of the pieces. The EpiPredictor, he says, enables them to see the board.

Researchers have linked many cancers to mutations in the DNA sequences of certain genes. Conversely, epigenetics enables 2 cells with identical DNA sequences to behave in completely different ways. This process is how people have specialized cells, such as nerve cells, bone cells, and blood cells, that have the same DNA but look and behave in unique ways.

A family of proteins called polycomb-group proteins are key epigenetic players in cancer. Found deep in the nuclei of cells, they have been shown to be present in high levels in some of the most aggressive forms of breast and prostate cancer. They can be called upon to silence any one of several hundred to several thousand genes by segments of DNA called polycomb response elements. To date, scientists have only been able to find a few polycomb response elements (2 in mice and 1 in humans), even though there are hundreds to thousands in any genome.

In tests on the genome of the fruit fly, Drosophila melanogaster, the EpiPredictor program found nearly 300 epigenetic target genes. Experimental research verified that the program's predictions were biologically significant.

Researchers are now working on using the method to scan the human genome to search for genes that may play a role in cancer epigenetics as well as to identify the location and function of genes in other areas beyond epigenetics.

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