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In a technical tour de force, Salk scientists take a global view of the epigenome

A collaboration between researchers at the Salk Institute for Biological Studies and the University of California at Los Angeles captured the genome-wide DNA methylation pattern of the plant Arabidopsis thaliana - the "laboratory rat" of the plant world - in one big sweep.

"In a single experiment we recapitulated 20 years worth of anecdotal findings and then some," says senior author Joseph Ecker, Ph.D., a professor in the Salk Institute's Plant Biology Laboratory. "Previously, only a hand full of plant genes were known to be regulated by methylation. In addition to those, we found hundreds of others."

These technological innovations, pioneered by Ecker's team and that of Steve Jacobsen, Ph.D., a Howard Hughes Medical Institute investigator at UCLA, should have broad impact on the analysis of the human genome, stem cell biology and therapeutic cloning. Their findings will appear in a forthcoming issue of Cell.

Our view of heredity has largely been written in the language of DNA, but recent discoveries in a field known as epigenetics - the study of heritable changes in gene function that occur without changing the letters of the DNA alphabet - show that how a cell "reads" those letters is critical.

Methylation is chemical modification of one letter C (cytosine) of the four letters (A, G, C, and T) reiterated in our DNA. Adding a bulky methyl group to a C often blocks interaction with proteins required to activate gene expression, effectively silencing the methylated gene.

Ecker and Jacobsen were funded by the National Human Genome Research Institute (NHGRI), which launched a public consortium known as ENCODE, for the Encyclopedia Of DNA Elements. Now that the human genome has been sequenced, ENCODE aims to develop technology to decipher what 30 million (1%) of those letters "spell" by identifying not only what genes they encode, but how epigenetic modifications switch genes off and on. Once that's achieved, the effort w
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Source:Salk Institute


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