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Simplifying Complexity - New Insights Into How Genomes Work
Date:4/1/2010

to play a melody, transcription factors bind to particular sites along a chromosome to turn nearby genes on or off. Decades of research have shown that the resulting patterns of gene expression direct a cell or organism's development, normal functioning, and responses to environmental challenges.

In addition, malfunctions in the genetic system can cause various diseases including cancer. "A disease might sometimes be considered an improper change in the dynamics of a network of interactions," says Képès. "So understanding their properties and how to correct or control their dynamics is essential."

Trolling for transcription factors
Until now, the most effective way researchers had to try to match genes and provisional transcription factors was to look for short DNA sequences that were known to bind to specific regulatory molecules. This approach remains useful, says Képès, but produces many false positives - potential regulatory relationships that prove false.

Following up on those false leads is wasteful. "Doing it with a pipette takes a long time and costs a lot of money," says Képès.

The GENNETEC team decided to address that problem by studying a new and independent way to predict whether a gene is controlled by a particular factor.

In earlier research, Képès and his colleagues discovered that genes that respond to the same transcription factor are often spaced regularly along a chromosome. They suspected that this periodic spacing is related to the way that DNA coils up inside the nucleus of a cell, and serves to optimise the functioning of related genes and transcription factors by grouping them geographically.

Scientists are always more comfortable if they understand the
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