Is "junk DNA" really junk?

The term "junk DNA" refers to the portion of the total DNA of any organism that (as far as anyone can tell) has no identifiable purpose -- that is, DNA that isn't part of a gene which codes for a protein or some type of non-coding RNA and isn't part of a regulatory region which controls the expression of a gene.

Whatever this junk DNA may be, the interesting thing is that there seems to be a lot of it, but the amount varies widely between species. There are hints, such as the research to be discussed here, that not all of the junk DNA really has no functional purpose. So a more neutral term like "non-coding DNA" might be more appropriate.

It is estimated that about 97% of human DNA is of the non-coding sort. Other species may have much more non-coding DNA or much less, and the amount seems to have little correlation to the complexity of the organism. The single-cell Amoeba dubia may have 200 times as much DNA in its genome, while the Fugu rubripes pufferfish genome is only about one tenth as large as the human genome, yet seems to have a comparable number of genes. Most of the difference between genomes is the result of non-coding DNA. (The wide variation in genome sizes is known as the C-value enigma.)

Where could all this "excess" DNA have come from? There are various possible sources. A major source is transposons or "jumping genes", which are DNA segments that easily move around or are copied within a genome. It is estimated that transposons (in original or mutated form) make up about 45% of the human genome. Another source is viruses and retroviruses, which reproduce by inserting their genetic material (DNA or RNA) into a host genome, with the help of an integrase enzyme. If this genetic material is inserted into a germline cell, it is copied to future generations (if the host survives).

Does this non-coding DNA have any useful function or purpose, and if so, what? Various studies have suggested that there is a function, in that some parts of it seem to be more strongly conserved in evolution than can be accounted for by chance. If it really didn't have a function, then specific sequences would by mutation become different in different species, and the more distant the relationship between two species, the more dissimilarity would be expected between their non-coding DNA.

This study suggests that indeed there is more similarity than would be expected:

UCSD Study Shows 'Junk' DNA Has Evolutionary Importance

In the October 20 issue of Nature, Peter Andolfatto, an assistant professor of biology at UCSD, shows that these non-coding regions play an important role in maintaining an organism’s genetic integrity. In his study of the genes from the fruit fly Drosophila melanogaster, he discovered that these regions are strongly affected by natural selection, the evolutionary process that preferentially leads to the survival of organisms and genes best adapted to the environment. ...

Using a recently developed population genetic approach, Andolfatto showed in his study that these expansive regions of "junk" DNA—which in Drosophila accounts for about 80 percent of the fly’s total genome—are evolving more slowly than expected due to natural selection pressures on the non-protein-coding DNA to remain the same over time.

"This pattern most likely reflects resistance to the incorporation of new mutations," he says. "In fact, 40 to 70 percent of new mutations that arise in non-coding DNA fail to be incorporated by this species, which suggests that these non-protein-coding regions are not 'junk', but are somehow functionally important to the organism."

So it looks like some of the non-coding DNA probably has a function. But what? Andolfatto's study wasn't designed to answer that important question. One can guess various possibilities, such as

• A large proportion of non-coding DNA reduces the chance that harmful mutations will affect functional DNA.
  
• At the same time, slight mutations to repeated copies of functional genes may result in modified genes that improve an organism's adaptation to its environment, without losing the original gene's function while it is still needed.
  
• There may be as yet unknown regulatory functions performed by certain DNA segments, which facilitate or inhibit the expression of real genes in environmentally-dependent circumstances.
  

The investigation of non-coding DNA seems likely to keep molecular biologists busy for some time to come.

Another article on this research: Time to stop trashing junk DNA

Much more information on junk DNA: EvoWiki article

Tags: junk DNA, non-coding DNA