'Junk' DNA Has Important Role, Researchers Find

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'Junk' DNA Has Important Role, Researchers Find

http://www.sciencedaily.com/releases/2009/05/090520140408.htm

Scientists have called it " junk DNA. " They have long been perplexed by these

extensive strands of genetic material that dominate the genome but seem to lack

specific functions. Why would nature force the genome to carry so much excess

baggage?

Now researchers from Princeton University and Indiana University who have been

studying the genome of a pond organism have found that junk DNA may not be so

junky after all. They have discovered that DNA sequences from regions of what

had been viewed as the " dispensable genome " are actually performing functions

that are central for the organism. They have concluded that the genes spur an

almost acrobatic rearrangement of the entire genome that is necessary for the

organism to grow.

It all happens very quickly. Genes called transposons in the single-celled

pond-dwelling organism Oxytricha produce cell proteins known as transposases.

During development, the transposons appear to first influence hundreds of

thousands of DNA pieces to regroup. Then, when no longer needed, the organism

cleverly erases the transposases from its genetic material, paring its genome to

a slim 5 percent of its original load.

" The transposons actually perform a central role for the cell, " said

Landweber, a professor of ecology and evolutionary biology at Princeton and an

author of the study. " They stitch together the genes in working form. " The work

appeared in the May 15 edition of Science.

In order to prove that the transposons have this reassembly function, the

scientists disabled several thousand of these genes in some Oxytricha. The

organisms with the altered DNA, they found, failed to develop properly.

Other authors from Princeton's Department of Ecology and Evolutionary Biology

include: postdoctoral fellows Mariusz Nowacki and Higgins; 2006 alumna

Genevieve Maquilan; and graduate student Estienne Swart. Former Princeton

postdoctoral fellow Doak, now of Indiana University, also contributed to

the study.

Landweber and other members of her team are researching the origin and evolution

of genes and genome rearrangement, with particular focus on Oxytricha because it

undergoes massive genome reorganization during development.

In her lab, Landweber studies the evolutionary origin of novel genetic systems

such as Oxytricha's. By combining molecular, evolutionary, theoretical and

synthetic biology, Landweber and colleagues last year discovered an RNA

(ribonucleic acid)-guided mechanism underlying its complex genome

rearrangements.

" Last year, we found the instruction book for how to put this genome back

together again -- the instruction set comes in the form of RNA that is passed

briefly from parent to offspring and these maternal RNAs provide templates for

the rearrangement process, " Landweber said. " Now we've been studying the actual

machinery involved in the process of cutting and splicing tremendous amounts of

DNA. Transposons are very good at that. "

The term " junk DNA " was originally coined to refer to a region of DNA that

contained no genetic information. Scientists are beginning to find, however,

that much of this so-called junk plays important roles in the regulation of gene

activity. No one yet knows how extensive that role may be.

Instead, scientists sometimes refer to these regions as " selfish DNA " if they

make no specific contribution to the reproductive success of the host organism.

Like a computer virus that copies itself ad nauseum, selfish DNA replicates and

passes from parent to offspring for the sole benefit of the DNA itself. The

present study suggests that some selfish DNA transposons can instead confer an

important role to their hosts, thereby establishing themselves as long-term

residents of the genome.

Journal reference:

Mariusz Nowacki, P. Higgins, Genevieve M. Maquilan, Estienne C. Swart,

G. Doak, and F. Landweber. A Functional Role for Transposases in a

Large Eukaryotic Genome. Science, 2009; 324 (5929): 935 DOI:

10.1126/science.1170023