By the Blouin News Science & Health staff

Scientists search for disease clues in “junk” DNA

by in Medicine, Research.

Scientists at the Swiss Federal Institute of Technology (EPFL) in Ecublens, near Lausanne, France on January 29, 2013

Scientists at the Swiss Federal Institute of Technology (EPFL) in Ecublens, near Lausanne, France on January 29, 2013 (REUTERS/Valentin Flauraud)

It’s looking more and more like human “junk” DNA — i.e., DNA with unknown function — may have been misnamed. In a January 2013 study, researchers at the Dana Farber Cancer Institute in Boston  used gene sequencing to find that two mutations in “junk” DNA were present in melanoma tumors.  The mutations are located in a section of DNA that controls whether the telomerase reverse transcriptase (TERT)  is switched on. This molecule is part of the enzyme telomerase, which, together with the RNA component with which it links, prolong the life of cells that would otherwise be near cell death. This is key in tumor growth: when on, the TERT gene can cause a cell to replicate almost endlessly. Since normal somatic cells do not express TERT, the argument runs, telomerase inhibition may slow cancer growth.  When the mutant DNA was attached to a part of a gene that codes for a protein, production of that protein was increased. The scientists presumed that the same thing would happen with TERT genes exposed to the mutant DNA.

So the term “junk” looks increasingly like an artifact of our as-yet-incomplete knowledge. According to a September 2012 Scientific American article, when scientists at the Human Genome Project presented the rough draft of DNA sequences in 2000, over 97 percent of the bases seemed to be gibberish or to have no specific function. Now scientists at the Encyclopedia of DNA Elements (ENCODE) Consortium, an international collaboration of research groups, are producing a list of previously hidden switches, signals and signposts embedded in junk DNA. The research shows that “junk” DNA is, in fact, involved in complex regulations of gene expression and evolution of regulatory elements. Indeed, fully 9 percent of DNA accounts for such regulatory elements — but ENCODE researchers think the figure may be closer to 20 percent, having found 10,000 stretches of DNA that code for RNA that does not result in protein formation.  According to Michael Snyder, a Stanford University researcher for the project, “Most of the changes that affect disease don’t lie in the genes themselves; they lie in the switches.”

According to Dr. Birney, it’s all about what we don’t know that we don’t know. Although the human genetic code final version was revealed in 2003, scientists at ENCODE say this is just the beginning of research to unravel DNA’s mysteries. ENCODE researchers generated 15 trillion bytes of raw data and analyzed it in the equivalent of more than 300 years of computer time. Since many disease switches are hidden in “junk” DNA, continuing research will offer clues as to the sources of disease and the creation of appropriate drugs to fight it.