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.

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.

9 Comments

1. 1. theDNAproblem 03:01 AM 9/6/12

   It is great that the theory of Junk DNA has been proven false. Logic tells us that there is a lot more information in the DNA than even this newly uncovered information. Here is a video outlining what has to be in the DNA:
   http://www.youtube.com/watch?v=Ub9_KEHGr4Q&feature=plcp or look for this on You Tube 02 Information in DNA by theDNAproblem.
   The process these scientists are involved in is what is known as reverse engineering in computing.
   

   Reply | Report Abuse | Link to this

2. 2. BuckSkinMan 11:46 AM 9/6/12

   
   So, there's a lot more to "junk science" than right wing ideologues would have us believe! Excellent! (just kidding, we know conservatives don't know anything about science... and a lot of other things)
   
   Actually, this discovery lends credence to the idea that "nature" holds secrets we're just beginning to notice or understand. It is good though that the idea of "junk DNA" has been found to be a false trail. DNA mapping no longer has a warning equivalent to the "here be dragons" legend said to have been on early maps.

   Reply | Report Abuse | Link to this

3. 3. denke42 04:15 PM 9/6/12

   Interesting analogy from NY Times article yesterday:
   
   “It’s Google Maps,” said Eric Lander, president of the Broad Institute, a joint research endeavor of Harvard and the Massachusetts Institute of Technology. In contrast, the project’s predecessor, the Human Genome Project, which determined the entire sequence of human DNA, “was like getting a picture of Earth from space,” he said. “It doesn’t tell you where the roads are, it doesn’t tell you what traffic is like at what time of the day, it doesn’t tell you where the good restaurants are, or the hospitals or the cities or the rivers.”
   
   The new result “is a stunning resource,” said Dr. Lander, who was not involved in the research that produced it but was a leader in the Human Genome Project. “My head explodes at the amount of data.”

   Reply | Report Abuse | Link to this

4. 4. john.fentress@gmail.com 05:43 PM 9/6/12

   Molecular biology is a wonderfully powerful field. But so many times the results in the past have been described as discovering "magic bullets", little pieces of this or that that act exclusively in the production of complex states. An unfortunate biproduct has been the frequent temptation to jump direct from parts of the protein coding genome to final "hardwired" products that affect entire lifetimes. In retrospect this was clearly bad science, not in terms of the new and powerful factual details uncovered, but in the mistaken assumptions that this was all the was to the story. Current research in epigenetics, of which so-called junk DNA is a major player by turning on and off protein producing genes, has begun to paint a more complex but clearly more relevant picture. There are many fields in biology where experimentally isolated parts of complexly integrated systems have led to a loss of intellectual reality that these isolated parts, in isolation, do not reveal their entire richness. It is good to see that a turn around in such narrow thinking is beginning to give may to more mature conceptualizations - as complex as these may turn out to be.

   Reply | Report Abuse | Link to this

5. 5. jh443 10:59 PM 9/6/12

   I am encouraged by these findings. Not only for the reasons cited by other commenters (to which I agree), but also because the possibility of being denied insurance coverage due to "faulty DNA" now seems far less likely - for a while at least.

   Reply | Report Abuse | Link to this

6. 6. slaven41 10:00 AM 9/7/12

   So, we need a new name for "junk dna." How about "proteinic" and "aproteinic" dna, for dna that encodes proteins and dna that doesn't encode proteins, respectively?
   
   Or, we'll just keep calling it junk dna, since that's what everyone is used to. That's how science is done. :-)

   Reply | Report Abuse | Link to this

7. 7. luhng 02:42 AM 9/12/12

   Junk DNA isnt the question here. The question is in fact the matter of a patern in all existance. this patern we find in all things.For example we have this groth that occures on a Birch tree that is a virus that eats the trees and kills them then spreding to another tree via air. Only one out of every 10,000 trees gets this CANCERous!!!! infestation!!! Now looking back at the human populous and using the same fractalated therory, as with the trees?????????? The CHAGA KILLS cancer!!! So we look at the mitachondrial DNA???? Welook at the star patern, time of birth andhow healthy or ill the body is at that time. through preasure point theropy and aroma theropy using meditative practices and drinking enough alkaline water to create an environment for cell reconstitution. One must eat plenty of fresh garden herbs that have high Hz levels. While on this regimen one must remember that there is a positive and negative, male and female, right and left, to everything. So to much of one thing can be as bad as to little of another. Balance must be achieved in the rebirth of the individuals lifestyle and the thought process has to equal the amount of energy applied to every day living. Repetition along with self programming initiates cell restructurization. So with a recipe derived from the makeup of one's DNA nano molecules can be produced and injected into the human body as a defense mechanism. Our very own little battle ships fighting disease inside us.One Might ask how can we build somthing so small? I say look at the cog wheel in a wind up watch...

   Reply | Report Abuse | Link to this

8. 8. luhng in reply to luhng 03:24 AM 9/12/12

   answer1: Fuel Oxidation and The Generation of ATP.
   
   answer2: Synthesis of DNA.
   
   answer3: Regulation of Gene Expression
   
   answer4: Use of Recombinant DNA Techniques in Medicine.
   
   ;)
   

   Reply | Report Abuse | Link to this

9. 9. DrJehr1 01:07 PM 9/13/12

   The concept of "junk" DNA always seemed foolish. Evolution wouldn't keep so much data if it were totally useless. Finally a little light has been shown on the situation.

   Reply | Report Abuse | Link to this