Vertebrate genomes are full of junk. Despite the occasional confusing magazine article, the spurious claims by creationists, or obfuscatory statements by some scientists, we know that our genomes are stuffed full of DNA sequence that serves no functional role for the organism. The vast bulk of this junk sequence consists of molecular parasites, called transposable elements, whose only 'function' is to replicate themselves. While our genomes obviously contain critical information required to build and maintain ourselves, they are also vast ecosystems of virus-like parasites that have colonized our DNA.
A recent paper in the journal Genome Research describes the DNA ecosystem of the opossum genome. "Ecosystem" is not an exaaggeration; more than 52% of the opossum genome is comprised of transposable elements, which can be classed into nearly 500 different families. Transposable elements are similar to viruses; they are, one way or another, able to replicate themselves within an organism's genome and get passed on to the next generation. These elements have variety of survival strategies; some elements get transcribed into RNA and then 'reverse transcribed' back into DNA and inserted somewhere in the genome, while other elements never go through an RNA stage. Some transposable elements encode proteins that enable them to spread through the genome more efficiently; other elements don't bother to code for any proteins and instead hijack the proteins produced by those elements that can code for them.
Why do transposable elements exist in our genomes? Because they can. If a DNA element in an organism's genome can get itself passed on into the next generation, whether that element is beneficial to the organism or not, then obviously it will remain in the genome of that species. Since these elements don't generally serve any functional role, there is no reason for natural selection to preserve them, and we thus see piles of defective copies of transposable elements scattered around our genomes. These elements no longer have the ability to spread through the genome and they serve no function - they are pure junk. While our cells do have systems that try to stop these elements from spreading, we, and most animals, have not evolved effective ways to get rid of the junk elements once they are there; these elements therefore hang around and bulk up our genomes with non-functional material. About 45% of the human genome consists of these elements; that fraction rises to 52% for the opossum (which has a genome slightly larger than ours).
Transposable elements are not completely useless. For one, biologists love them because they can be helpful for studying evolutionary history - one approach to teasing out relationships among various species is to reconstruct a rough history of transposable element activity in various genomes. We have also known for some time that these elements can occasionally be recruited for a functional role (such as telemoeres in flies, X-chromosome inactivation in mammals, and centromeres in various organisms).
The opossum paper offers even more tantalizing, although not wholly unprecedented, evidence of a larger role for transposable elements. The authors of this paper looked at transposable elements, common to both opossum and human, that were present in known or suspected regulatory regions of the genome. Transposable elements in these regions are obvious candidates for a functional role. And remarkably, the researchers found that a handful of transposable element families were highly abundant in these regulatory regions - in one case, 70% of all the individual elements of one family were found in regulatory regions of the genome. It is possible that this particular family of transposable elements somehow contains a useful 'regulatory module,' some sequence that has been recruited through evolution to control the expression some genes. If this is true, than this would be a case of transposable elements providing the raw genetic material to create new layers of regulation in the genome.
So while most of the self-perpetuating transposable element ecosystem is undoubtedly junk from the perspective of the organism hosting it, our genomes are occasionally able to scoop up some of the detritus and put it to good use.