"Junk" DNA Proves to be Highly Valuable
Flores June 2, 2009
What was once thought of as DNA with zero value in plants--dubbed
"junk" DNA--may turn out to be key in helping scientists improve the control of
gene expression in transgenic crops.
That's according to Agricultural
Research Service (ARS) plant pathologist
Cooper at the agency's
Genomics and Improvement Laboratory in Beltsville, Md., and collaborators
at Johns Hopkins University in Baltimore, Md.
For more than 30 years, scientists have been perplexed by the workings
of intergenic DNA, which is located between genes. Scientists have since found
that, among other functions, some intergenic DNA plays a physical role in
protecting and linking chromosomes. But after subtracting intergenic DNA, there
was still leftover or "junk" DNA which seemed to have no purpose.
Cooper and collaborators investigated "junk" DNA in the model plant
Arabidopsis thaliana, using a computer program to find short segments of
DNA that appeared as molecular patterns. When comparing these patterns to
genes, Cooper's team found that 50 percent of the genes had the exact same
sequences as the molecular patterns. This discovery showed a sequence pattern
link between "junk" and coding DNA. These linked patterns are called pyknons,
which Cooper and his team believe might be evidence of something important that
drives genome expansion in plants.
The researchers found that pyknons are also the same in sequence and
size as small segments of RNA that regulate gene expression through a method
known as gene silencing. This evidence suggests that these RNA segments are
converted back into DNA and are integrated into the intergenic space. Over
time, these sequences repeatedly accumulate. Prior to this discovery, pyknons
were only known to exist in the human genome. Thus, this discovery in plants
illustrates that the link between coding DNA and junk DNA crosses higher orders
of biology and suggests a universal genetic mechanism at play that is not yet
The data suggest that scientists might be able to use this information
to determine which genes are regulated by gene silencing, and that there may be
some application for the improvement of transgenic plants by using the pyknon
This research was published online as an advance article on the
website, and will be published later this year in a special issue of
Computational Systems Biology.
ARS is the principal intramural scientific research agency of the
U.S. Department of