“Junk” DNA holds clues to cancer, autism

With the latest annotation of the human genome, researchers have made new discoveries about common diseases

Topics: Scientific American, Human Genome, Science, Autism, Cancer, Medicine,

"Junk" DNA holds clues to cancer, autism
This article originally appeared on Scientific American.

When the draft of the human genome was published in 2000, researchers thought that they had obtained the secret decoder ring for the human body. Armed with the code of 3 billion basepairs of As, Ts, Cs and Gs and the 21,000 protein-coding genes, they hoped to be able to find the genetic scaffolds of life—both in sickness and in health.

Scientific American But in the 12 years since then, very few diseases—almost all of them very rare—have been linked definitively to changes in the genes themselves. And large, genome-wide studies searching for genetic underpinnings for more common diseases, such as lung cancer or autism, have pointed to the nether regions of the genome between the protein-producing genes—areas that were often thought to contain“junk” DNA that was not part of the pantheon of known genes.

An international consortium of hundreds of scientists has now deciphered a large portion of the strange language of this junk DNA and found it to be not junk at all. Rather it contains important signals for regulating our genes, determining disease risk, height and many of the other complex aspects of human biology that make each one of us different. The findings are described in 30 linked papers published online September 5 in Nature and other journals and described at the consortium’s Web site. (Scientific American is part of Nature Publishing Group.)

Called the Encyclopedia of DNA Elements (ENCODE), the group is focused on understanding not just the elements of the genome but also how they work together. “The complexity of our biology resides not in the number of our genes but in the regulatory switches,” Eric Green, director of the National Human Genome Research Institute and collaborator on the ENCODE project, said in a press briefing September 5. Through more than 1,600 separate experiments, analysis of more than 140 cell types and a massive amount of data analysis, the group found about 4 million of these so-called switches and can now assign functions to more than 80 percent of the entire genome. Compare that to the roughly 2 percent of the genome that is responsible for the protein-coding genes that researchers have been relying on to look for diseases and traits. “The genome project was about establishing the set of letters that make up the blueprint,” Green said. “When we finally put that blueprint together, we realized we could only really understand very little of it.”

These newly catalogued switches not only activate and de-activate genes, but also control how much of each protein gets made and when. They are involved in epigenetic changes, such as DNA methylation, which has been implicated in cardiovascular disease and other conditions. The new data promise to improve our understanding of many common diseases that might have similar genetic underpinnings. Genome-wide association studies (GWAS) have continuously come up short in identifying specific genes for common diseases, John Stamatoyannopoulos, associate professor of genome sciences at the University of Washington School of Medicine and ENCODE collaborator, said in the briefing. “Frustratingly, about 95 percent of information from these studies has been pointing to regions of the genome that do not make proteins,” he said. But, now with the ENCODE data, they can begin to decipher what genetic switches and functions might be common within and among these diseases. “We’re now exploring previously hidden connections between diseases that may explain similar clinical [symptoms],” he noted.

It will most likely be some time before these new findings, which are freely available, are put to use in approved therapies. “The pharmaceutical industry has largely given up on the genome,” Stamatoyannopoulos said. “And I think this is going to tremendously reinvigorate the utility of the genome.” These additional genetic elements, however, are already in use for screening and testing for diseases such as breast cancer, prostate cancer and autoimmune diseases, Richard Myers, president of HudsonAlpha Institute for Biotechnology in Ala., noted in the briefing.

The group has funding to continue their efforts and does not anticipate a slowdown in discoveries going forward. “Our blueprint is remarkably complicated, and we need to be committed for the long haul to understand it,” Green said. Compared with the publication of draft human genome 12 years ago—and with initial findings from the ENCODE project published over the past several years—”the questions that we can now ask are more sophisticated,” Green said. And hopefully, those better questions will lead to more satisfying and medically useful answers.

More Related Stories

Featured Slide Shows

  • Share on Twitter
  • Share on Facebook
  • 1 of 17
  • Close
  • Fullscreen
  • Thumbnails
    John Stanmeyer

    Overdevelopment, Overpopulation, Overshoot

    Container City: Shipping containers, indispensable tool of the globalized consumer economy, reflect the skyline in Singapore, one of the world’s busiest ports.

    Lu Guang

    Overdevelopment, Overpopulation, Overshoot

    Man Covering His Mouth: A shepherd by the Yellow River cannot stand the smell, Inner Mongolia, China

    Carolyn Cole/LATimes

    Overdevelopment, Overpopulation, Overshoot

    Angry Crowd: People jostle for food relief distribution following the 2010 earthquake in Haiti

    Darin Oswald/Idaho Statesman

    Overdevelopment, Overpopulation, Overshoot

    “Black Friday” Shoppers: Aggressive bargain hunters push through the front doors of the Boise Towne Square mall as they are opened at 1 a.m. Friday, Nov. 24, 2007, Boise, Idaho, USA

    Google Earth/NOAA, U.S. Navy, NGA, GEBCO

    Overdevelopment, Overpopulation, Overshoot

    Suburban Sprawl: aerial view of landscape outside Miami, Florida, shows 13 golf courses amongst track homes on the edge of the Everglades.

    Garth Lentz

    Overdevelopment, Overpopulation, Overshoot

    Toxic Landscape: Aerial view of the tar sands region, where mining operations and tailings ponds are so vast they can be seen from outer space; Alberta, Canada

    Cotton Coulson/Keenpress

    Overdevelopment, Overpopulation, Overshoot

    Ice Waterfall: In both the Arctic and Antarctic regions, ice is retreating. Melting water on icecap, North East Land, Svalbard, Norway

    Yann Arthus-Bertrand

    Overdevelopment, Overpopulation, Overshoot

    Satellite Dishes: The rooftops of Aleppo, Syria, one of the world’s oldest cities, are covered with satellite dishes, linking residents to a globalized consumer culture.

    Stephanie Sinclair

    Overdevelopment, Overpopulation, Overshoot

    Child Brides: Tahani, 8, is seen with her husband Majed, 27, and her former classmate Ghada, 8, and her husband in Hajjah, Yemen, July 26, 2010.

    Mike Hedge

    Overdevelopment, Overpopulation, Overshoot

    Megalopolis: Shanghai, China, a sprawling megacity of 24 Million

    Google Earth/ 2014 Digital Globe

    Overdevelopment, Overpopulation, Overshoot

    Big Hole: The Mir Mine in Russia is the world’s largest diamond mine.

    Daniel Dancer

    Overdevelopment, Overpopulation, Overshoot

    Clear-cut: Industrial forestry degrading public lands, Willamette National Forest, Oregon

    Peter Essick

    Overdevelopment, Overpopulation, Overshoot

    Computer Dump: Massive quantities of waste from obsolete computers and other electronics are typically shipped to the developing world for sorting and/or disposal. Photo from Accra, Ghana.

    Daniel Beltra

    Overdevelopment, Overpopulation, Overshoot

    Oil Spill Fire: Aerial view of an oil fire following the 2010 Deepwater Horizon oil disaster, Gulf of Mexico

    Ian Wylie

    Overdevelopment, Overpopulation, Overshoot

    Slide 13

    Airplane Contrails: Globalized transportation networks, especially commercial aviation, are a major contributor of air pollution and greenhouse gas emissions. Photo of contrails in the west London sky over the River Thames, London, England.

    R.J. Sangosti/Denver Post

    Overdevelopment, Overpopulation, Overshoot

    Fire: More frequent and more intense wildfires (such as this one in Colorado, USA) are another consequence of a warming planet.

  • Recent Slide Shows



Comment Preview

Your name will appear as username ( settings | log out )

You may use these HTML tags and attributes: <a href=""> <b> <em> <strong> <i> <blockquote>