Charting the epigenome( LA JOLLA CA Until recently the chem...)

LA JOLLA, CA Until recently, the chemical marks littering the DNA inside our cells like trees dotting a landscape could only be studied one gene at a time. But new high-throughput DNA sequencing technology has enabled researchers at the Salk Institute for Biological Studies to map the precise position of these individual DNA modifications throughout the genome of the plant Arabidopsis thaliana, and chart its effect on the activity of any of Arabidopsis roughly 26,000 genes.

For a long time the prevailing view held that individual modifications are not critical, says Joseph Ecker, Ph.D., a professor in the Plant Biology laboratory and director of the Salk Institute Genomic Analysis Laboratory. The genomes of higher eukaryotes are peppered with modifications but unless you can take a detailed look at a large scale there is no way of knowing whether a particular mark is critical or not.

The Salk study, which appears today in the online issue of Cell, paints a detailed picture of a dynamic and ever-changing, yet highly controlled, epigenome, the layer of genetic control beyond the regulation inherent in the sequence of the genes themselves.

Being able to study the epigenome in great detail and in its entirety will provide researchers with a better understanding of plant productivity and stress resistance, the dynamics of the human genome, stem cells capacity to self-renew and how epigenetic factors contribute to the development of tumors and disease.

Discoveries in recent years made it increasingly clear that there is far more to genetics than the sequence of building blocks that make up our genes. Adding molecules such as methyl groups to the backbone of DNA without altering the letters of the DNA alphabet can change how genes interact with the cells transcribing machinery and hand cells an additional tool to fine-tune gene expression.

The goal of our study was to integrate multiple levels of epigenetic informatio
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