Junk DNA may not be so ‘junky’ after all

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 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 Evolutionary Biology 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 DNA transposons can instead confer an important role to their hosts, thereby establishing themselves as long-term residents of the genome.

Comments

  1. Dov Henis Dov Henis Israel says:

    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"
    www.princeton.edu/main/news/archive/S24/28/32C04/


    B. From "Aging Seen Without The Emperor'S New Clothes"
    www.sciencenews.org/.../Old_age_causes_problems_for_gut_cells
    www.articlesbase.com/.../...ew-clothes-808441.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
    www.physforum.com/index.php
    www.the-scientist.com/.../122.page#2321

  2. Dov Henis Dov Henis Israel says:

    Science Blindness To Gene's Lifehood

    A. From "Better sensing through empty receptors"

    www.sciencenews.org/.../Better_sensing_through_empty_receptors

    A new model suggests cells may be more sensitive to their environment than previously thought.

    This work deals with the mechanism and efficiency of some components of the sensing system on a monocell organism's outer membrane. It refers to

    - cells may benefit...
    - how a cell sorts information...
    - single-celled organisms, such as bacteria and yeast, must accurately judge their landscape to find food and avoid trouble.


    B. From "Bacterium With Chemoreceptors Versus Multicelled Organisms"

    www.the-scientist.com/.../122.page#3489

    From sensing to signalling to tumbling to re-swimming. This goes on in a bacterial cell. Who and how assesses the information and draws and issues instructions?


    C. 21st Century Science Is Still Blind To Gene's Lifehood

    This blindness is one of the hallmarks of the scientifically decadent corrupt still ongoing 20th century technology culture.


    D. Cells are just the functional housings of the organisms genes-genome

    Nature evolved genes to constrain energy as long as possible and to replicate for augmenting the amount of constrained energy.

    Genes evolved the capability and technique first to adapt and later to manipulate their environments by means of their expressions. Their expressions handle everything for the genes, from sensing to remembering to signaling through foraging through all components of surviving. Each and all of their expressions are targeted for augmented constrained energy survival.

    Is this so difficult to notice and accept scientifically?

    It seems that mundane scientific decadence blinds 21st century science to the lifehood of genes.

    Dov Henis
    (Comments From The 22nd Century)
    Updated Life's Manifest May 2009
    www.the-scientist.com/.../122.page#2321
    Implications Of E=Total[m(1 + D)]
    www.the-scientist.com/.../122.page#3108

    • Dov Henis Dov Henis Israel says:

      Watch Evolution Unfold


      Time In A Bottle: Scientists Watch Evolution Unfold
      www.sciencedaily.com/.../091018141716.htm


      - "demonstrates natural selection at work"

      Natural selection is involved only in a small fraction of evolution, in cases of genetic accidents. Normal evolution is an evolution of culture, of reaction to circumstances, fed back to the genes, who consequently modify their expressions accordingly, by way of alternative splicing.

      - "By the 20,000-generation midpoint, researchers discovered 45 mutations among surviving cells"

      They did not "discover", but uncover, the "mutations", which were not mutations but alternatively spliced genes in response to the conditions of the culture. (It is not a coincidence that a community of monocell organisms is termed a culture. It is a culture just as a community of multicell organisms).

      - "Those mutations, according to Darwin's theory, should have conferred some advantage, and that's exactly what the researchers found."

      What the reserchers uncovered (not found, no more found than Columbus found America when stumbling upon it) is NOT "mutations that conferred advantage". They uncovered what has been known and explained for the past several years, i.e. that cultural advantages induced genetic changes, manifest in the form of changed expressions of genes.


      It seems that mundane scientific decadence blinds 21st century science to the lifehood of genes.

      Dov Henis
      (Comments From The 22nd Century)
      Updated Life's Manifest May 2009
      www.the-scientist.com/.../122.page#2321
      Implications Of E=Total[m(1 + D)]
      www.the-scientist.com/.../122.page#3108

The opinions expressed here are the views of the writer and do not necessarily reflect the views and opinions of News Medical.
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