Simplifying complexity — new insights into how genomes work

Posted: April 3, 2010 at 10:29 pm

Story Summary: com) — A genome is a complex system of genes and factors that regulate them. A European research team has clarified how such dynamic systems work, leading to a new way to predict genetic regulators. Their findings promise to boost research into the functioning of genetic networks in general, and into the dynamics of the human genetic system in health and disease. Decades of research have shown that the resulting patterns of gene expression direct a cell or organisms development, normal functioning, and responses to environmental challenges. Trolling for transcription factorsUntil 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. Doing it with a pipette takes a long time and costs a lot of money, says Kepcs. 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. 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 factorsby grouping them geographically. Scientists are always more comfortable if they understand the mechanism that produces an observed regularity. What we discovered is that there is a clear link between chromosome structure and gene expression, says Kepcs, a link that we can now predict in a very precise and workable way. Faster, more focused searchWhen the GENNETEC team combined their new positional predictor with the standard sequence predictor, they found that they could identify new gene-regulator relationships far more efficiently. Combining the two predictors allows us to predict the regulators of a particular gene much better, by cutting down on the false hits, says Kepcs. One of the consortium partners, NorayBio, based in northern Spain, is developing a commercial software package that will allow researchers worldwide to apply this more powerful approach to deciphering genetic networks. While Kepcs is pleased with this new research tool, he emphasises that the consortiums fundamental research on complex systems is equally important. Cells have just one genome, but with that one genome they can cope with multiple challenges, says Kepcs. We can use this biological solution as inspiration to make a new generation of algorithms to address complex problems better than before. The system is apparently controlled by a key protein that the researchers have named NINJA….Read the Full Story

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