DNA Junkyard Turns Treasure-Trove

Ms. Davies

September 9, 2012

Core Biology I Honors / C-Block, Davies

Current Event Report: DNA Junkyard Turns Treasure-Trove

Kolata, Gina. “Bits of Mystery DNA, Far From ‘Junk,’ Play Crucial Role” New York Times Online. 5 Sept 2012. <http://www.nytimes.com/2012/09/06/science/far-from-junk-dna-dark-matter-proves-crucial-to-health.html>

            The human genome is about 3 billion (3 x 10⁹) nucleotide base-pairs long. (U.S. Department of Energy Genome Programs, 2008) However, until now, scientists thought that only about 1% of the DNA had any function. This is because the approximately 20,000 genes sequenced by the human genome project in 2003 make up about 1% of the DNA. The rest of the DNA is referred to as “junk” or “noncoding DNA” in most textbooks and was thought to have little to no useful function. It was often thought to be left-over garbage from our evolutionary past, such as bits of ancient genes that have since lost their function. It was also posited that the DNA “junk” helped to protect the important information coded in our genes by providing a sort of buffer zone between genes and protecting them from the wear and tear that happens in the DNA replication in mitosis. For example, as we age our telomeres wear down with edge, encroaching on the important information coded in chromosomes. The gradual wearing down of our telomeres is thought to have something to do with the aging process. However, the hypothesis that “junk DNA” was simply there as a buffer, or a vestigial evolutionary remnant, is now “junk” itself. Now, thanks to research from project Encode, Encyclopedia of DNA Elements, which is providing a sort of roadmap of how genes are interconnected, scientists have discovered that “at least 80 percent of this DNA is active and needed” and “at least four million gene switches reside in bits of DNA that one were dismissed as ‘junk.’” (Kolata 2012)

                This finding has enormous implications for many genetically-linked diseases. Although some genetic diseases have a simple genetic cause (such as Huntington’s Disease or sickle-cell anemia), for a long time scientists have realized that some diseases have a genetic component, but one that is influenced by the environment. The field of epigenetics is the study of how genes are switched “on” and “off” by other genes or environmental factors. Many “switches” for genes are being discovered in the dark matter of DNA that was thought to have no function. This can lead to insights for complex diseases such as autism, psychiatric disorders, and cancer. Scientists have often been flummoxed by the complicated genetic components of some cancers. Cancer-linked genes can be switched on and off in a way that is not fully understood. Learning more about the dark matter of DNA may help shed light on epigenetic changes that contribute to certain cancers. As a genetic cancer researcher myself who focuses on epigenetics of pancreatic cancer, this discovery has major implications for my own research. I have been focusing on genes in stretches of DNA that are methylated (epigenetically modified) in unusual frequency in pancreatic cancer, to discover which genes might be important in the progression and treatment of this cancer. However, what I have failed to ask is HOW these genes get methylated in the first place. Perhaps it is due to unknown switches in the DNA formerly known as “junk.”

            Although I am aware that the New York Times is for a generally lay audience, I felt that the author, Gina Kolata, could have done more to explain some of the basic science behind this significant discovery. First of all, Kolata failed to mention project Encode, until the tenth paragraph, and even then, failed to describe exactly what the project is doing except by analogy. I would like to know more about the actual science behind project Encode, and what techniques make it more sophisticated that the Human Genome Project. Secondly, there was no mention as to how this new understanding will affect our perception of evolution. Junk DNA was often used as one of the pieces of evidence for evolution, and I question how evolutionary biologists and genetics will now reevaluate “junk DNA” in light of these discoveries. There were many other important ideas mentioned in this article, but none of them were discussed at length. Perhaps with over thirty scientific papers being published on this topic, it was simply too much to be encapsulated in one New York Times article. I hope that the New York Times will continue to print more on this discovery, and do it justice, as this is a virtual revolution in our understanding of genetics. With this discovery all of our biology and genetics textbooks are out of date and will have to be rewritten. The name “junk DNA” should be stricken from every index and in place a new term will have to substitute. Some have suggested “dark matter DNA,” however as we learn to unravel the mysteries of this region that comprises the majority of our DNA, perhaps we can come up a better term that better captures its importance.

U.S. Department of Energy Genome Programs. “The Science Behind the Human Genome Project.” 26 Mar 2008. <http://www.ornl.gov/sci/techresources/Human_Genome/project/info.shtml>