Research team finds important role for junk DNA

May 20, 2009 by Kitta MacPherson
Princeton scientists are probing the genetics of the pond organism Oxytricha, shown here in the process of reproducing. (Photo: Robert Hammersmith)

(PhysOrg.com) -- 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 of a pond organism have found that junk DNA may not be so junky after all. They have discovered that from regions of what had been viewed as the "dispensable " 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 , paring its genome to a slim 5 percent of its original load.

"The transposons actually perform a central role for the cell," said Laura 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 include: postdoctoral fellows Mariusz Nowacki and Brian Higgins; 2006 alumna Genevieve Maquilan; and graduate student Estienne Swart. Former Princeton postdoctoral fellow Thomas 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 transposons can instead confer an important role to their hosts, thereby establishing themselves as long-term residents of the genome.

Source: Princeton University (news : web)

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User comments : 4

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superhuman
not rated yet May 20, 2009
The label junk DNA is a testament to junk science.

It is obvious to anyone who actually understands evolution that no organism can ever contain 90% of useless DNA. It is simply impossible. Unused DNA would be lost in a very short time frame as it's maintenance incurs huge costs.
HenisDov
not rated yet May 21, 2009
Junk DNA, Junk Body Parts
It Is The Lifehood Of Genes That Makes All Organisms Alive
Are Parts Of Our Humanoid Body Superfluous Junk


A. "Research team finds important role for junk DNA"
http://www.prince...8/32C04/


B. From "Aging Seen Without The Emperor'S New Clothes"
http://www.scienc...ut_cells
http://www.articl...441.html

Right they are: "Nearly all organisms experience aging". But why "nearly"?

Why doesn't "science" accept the obvious fact that genes are organisms and "experience aging", too?

Not only yeast, worms and people. Also genes and the interdependent-genes-communes, genomes. Theye are both organisms. They are alive. It is their "lifehood" that makes us and all life forms "alive".

By plain common sense - my favorite scientific approach - they should also be "experiencing aging"...


C. If it is not the lifehood of genes that makes each and all organisms alive,

what otherwise makes each and all organisms alive?


Dov Henis
(Comments From The 22nd Century)
Updated Life's Manifest May 2009
http://www.physfo...ic=14988&st=495&#entry412704
http://www.the-sc...age#2321
Sean_W
5 / 5 (1) May 21, 2009
I suspect that even the researchers who still use the term "junk" do so for historical reasons not because they think it is "junk". I would also not be surprised if the term "junk" is not much more prevalent in popular science writing than in discourse between scientists. I read and hear terms like "non-coding" (itself not a perfect term) much more than I encounter the term "junk DNA".
PPihkala
5 / 5 (1) May 21, 2009
As far as I have understood junk DNA, that naming arose when first studies of genetic information indicated that only under 10% of DNA codes for proteins. Then it was thought that only proteins can have an active role. Now most should understand that this rest of genetic code is for making RNA that can influence how much proteins the protein coding DNA makes. And by varying the amount and timing of proteins they have a great power to change the workings of life.

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