Article: In A Technical Tour De Force, Scientists Take A Global View Of The Epigenome

In A Technical Tour De Force, 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 will be scaled up to learn more about the
dynamics of the whole human genome.

The approach developed by Ecker and collaborators may allow researchers to
do just that. "We fit the whole Arabidopsis genome - about 120 million
bases - on a single high density microarray," says Ecker. "To look at the
entire human genome you would just need six more chips."

Each microarray or DNA chip is dotted with 6 million short DNA fragments
that span the Arabidopsis genome like floor tiles. The researchers first
isolated all methylated DNA from plant cells and located where those
fragments fell on the array. Then they determined which genes were active
and which ones weren't in order to compare gene activation with the
methylation pattern.

The investigators saw significant changes when they compared activity of
genes in normal plants with gene activity in plant mutants unable to
methylate DNA. "It was pretty dramatic. There are hundreds of genes that you
never see expressed except in methylation mutants," says Ecker.

Almost a third of Arabidopsis' ~ 26,000 genes were methylated in some
manner, and where they were methylated determined the effect. As in mammals,
methylation in regulatory regions next to genes generally silenced genes.
However, methylation across the body of a gene appeared to correlate with
higher expression.

Different cell types show different methylation patterns. DNA methylation in
stem cells differs from that in a mature skin or nerve cell. Part of the
makeover mature cells must undergo for therapeutic cloning purposes will
likely involve remodeling methylation patterns to resemble those of stem
cells. And disease states, ranging from retardation to cancer, are marked by
aberrant methylation: some carcinogens cause cancer by methylating the
"wrong" genes, leading to uncontrolled growth.

Once a cell's DNA methylation pattern - be it normal or pathological - is
established, methylated sites are faithfully inherited by daughter cells.
The ability to take a high-resolution snapshot of what genes are methylated
and which ones aren't during different developmental or disease states might
show how cells self-renew or growth control genes become de-regulated.

The investigators also found that methylation silences transposons,
so-called "jumping genes," which can wreak genomic havoc by hopping about
the chromosomes. In the words of Ecker, undermethylated transposons "just go
wild," suggesting that mother nature keeps transposons in time-out by
covering them with methyl groups.

In addition to funding from NHGRI, this work was also supported by the
National Science Foundation's Arabidopsis 2010 Project - an effort to
identify functions for all Arabidopsis genes.

Other authors contributing to the study include Salk investigators Junshi
Yazaki, Ph.D., a postdoctoral researcher, graduate student Ambika
Sundaresan, and research associates Paul Shinn and Huaming Chen. Other
collaborators at UCLA include assistant professor Matteo Pellegrini, Ph.D.,
postdoctoral researchers Xiaoyu Zhang, Ph.D., Ian Henderson, Ph.D., and
Simon Chan, Ph.D., and research assistant Shawn Cokus.

The Salk Institute for Biological Studies in La Jolla, California, is an
independent nonprofit organization dedicated to fundamental discoveries in
the life sciences, the improvement of human health and the training of
future generations of researchers. Jonas Salk, M.D., whose polio vaccine all
but eradicated the crippling disease poliomyelitis in 1955, opened the
Institute in 1965 with a gift of land from the City of San Diego and the
financial support of the March of Dimes.

Source: Salk Institute
http://www.sciencedaily.com/releases/2006/09/060901164219.htm

Posted by
Robert Karl Stonjek


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