Forget the Democrats: The Real News Is No Junk DNA in Human Genome

Well, actually very damned little junk DNA in the human genome. Back in the 20th century as the human genome was being sequenced researchers were betting that it must take around 100,000 genes to make something as complicated as a homo sapiens. The official Genesweep bet eventually settled on around a mere 21,000. That's less than half the number it takes to make a corn plant. So most of the genome was thought to be filled up with "junk DNA" that kind of sat around cluttering up the place.

Since 2003, the Encyclopedia of DNA Elements or ENCODE project has been sifting through all those apparently useless base-pairs and it turns out that many of them are regulatory sequences that are largely devoted to telling genes what to do. From the press release:

...researchers linked more than 80 percent of the human genome sequence to a specific biological function and mapped more than 4 million regulatory regions (emphasis added) where proteins specifically interact with the DNA. These findings represent a significant advance in understanding the precise and complex controls over the expression of genetic information within a cell. The findings bring into much sharper focus the continually active genome in which proteins routinely turn genes on and off using sites that are sometimes at great distances from the genes themselves. They also identify where chemical modifications of DNA influence gene expression and where various functional forms of RNA, a form of nucleic acid related to DNA, help regulate the whole system.

“During the early debates about the Human Genome Project, researchers had predicted that only a few percent of the human genome sequence encoded proteins, the workhorses of the cell, and that the rest was junk. We now know that this conclusion was wrong,” said Eric D. Green, M.D., Ph.D., director of the National Human Genome Research Institute (NHGRI), a part of the National Institutes of Health. “ENCODE has revealed that most of the human genome is involved in the complex molecular choreography required for converting genetic information into living cells and organisms.” ...

“We were surprised that disease-linked genetic variants are not in protein-coding regions,” said Mike Pazin, Ph.D., an NHGRI program director working on ENCODE. “We expect to find that many genetic changes causing a disorder are within regulatory regions, or switches, that affect how much protein is produced or when the protein is produced, rather than affecting the structure of the protein itself.  The medical condition will occur because the gene is aberrantly turned on or turned off or abnormal amounts of the protein are made.  Far from being junk DNA, this regulatory DNA clearly makes important contributions to human health and disease.”  

Ain't science grand!?

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  • Jerry on the road||

    4 million regulatory regions

    Your DNA, you didn't build that.

  • Scarecrow Repair||

    Mama and papa did!

  • Alan Vanneman||

    Actually, this "grand" science was brought to you by "an immense federal project involving 440 scientists from 32 laboratories around the world," according to the New York Times (emphasis added, link below). Just sayin'

    http://www.nytimes.com/2012/09.....h.html?hpw

  • ||

    Well, actually very damned little junk DNA in the human genome

    Natural selection could have told you that.

    Also should note that my professors at college told us in the 90s that they probably weren't junk and most likely were involved in regulating sequencing and other odd jobs in the cell.

    This is not all that big of "discovery" as it has been suspected for some time.

  • Ron Bailey||

    Corning: Party pooper. Back in the day, one theory was that a lot of the "junk DNA" consisted of parasitic sequences that did not interfere with the operation of the actual genes and so could continue to multiply themselves over time.

    And yet, the insight of your professors is what led the ENCODE project. In any case, I supply a comment from the NY Times report:

    The big surprise was not only that almost all of the DNA is used but that a large proportion of it is gene switches. Before Encode, said Dr. John Stamatoyannopoulos, a University of Washington scientist who was part of the project, “if you had said half of the genome and probably more has instructions for turning genes on and off, I don’t think people would have believed you.”

  • Metazoan||

    Well, a lot of those parasitic sequences are silenced epigenetically, no?

  • ||

    Some are, some aren't.

  • ||

    Plus why would parasitic sequences not be like any other mutation. In most cases if they are not beneficial they would have been selected out.

    Hard to imagine huge portions of the genome being replicated over an over again giving no benefit and yet not make the organism less fit.

    hell by just having them in there they can cause damage by transposing themselves to other parts of the sequence.

    Reordering DNA is cool in movies...when it happens in real life organisms it more often then not means death. Less DNA would lower the chance of this considerably.

  • OldMexican||

    Re: Corning,

    Hard to imagine huge portions of the genome being replicated over an over again giving no benefit and yet not make the organism less fit.


    Just like those embryonic gills. It's not like we need them to find sunken submarines and cities when the caps melt...

  • ||

    Embryonic gills are not 99% of the human genome.

    Same with tonsils or appendix.

    Seriously Old Mex when a cell replicates DNA it costs energy. Do you think an organism that wasted 99% of that expenditure on doing nothing would last all that long in the wild competing against organisms that didn't?

    Embryonic gills are not very expensive to an organism...especially considering that the cells that form them eventually become lungs.

  • Cytotoxic||

    It's easier to select something out that doesn't replicate itself. Transposons do just that and there are a lot of them although a great deal of epigenetic silencing goes on. Pretty fascinating to think about. It's like an immune system within each cell at the DNA level.

    There is still 'junk' DNA consisting of old integrated viruses and human genes that are accidentally put back in by misguided transposon integrases. The advantage of this stuff is that it is good material to evolve with.

  • ||

    Transposons do just that and there are a lot of them although a great deal of epigenetic silencing goes on.

    I was thinking of when a tranposon inserts itself in a very bad place...like a large addition inside of an encoding sequence.

    Epigenetic silencing cannot protect against that. If a cell can't produce a vital protein it is a dead cell. Though I imagine most vital proteins have redundant DNA sequences.

  • SKR||

    Well not in humans that we know of, but parasitic sections could be parasitic. There are parasitic plants that steal and/or transfer genes from/to their host plants. It is not unreasonable to conjecture that a particular chunk of data could be purposely detrimental.

  • ||

    It is not unreasonable to conjecture that a particular chunk of data could be purposely detrimental.

    No, but 99% of the entire genome being parasitic seems a bit unlikely.

  • SKR||

    Well yeah sure.

  • ||

    Before Encode, said Dr. John Stamatoyannopoulos, a University of Washington scientist who was part of the project, “if you had said half of the genome and probably more has instructions for turning genes on and off, I don’t think people would have believed you.”

    Oh shit...

    Well seeing as how I went to UW the idea that it was not Junk may not have been as widespread as I thought it was.

  • Bill||

    I also thought a lot of it was repetitive sequences that might be involved in recombination events.

    And the introns are not coding or regulatory but involved in splicing (also recombination).

    I'll have to check out the paper. I have to teach this stuff next month.

  • Cytotoxic||

    Introns can be regulatory. They can form secondary structures that interfere with translation, and sometimes they are bizzarely self-splicing.

  • ||

    I remember the very same.

  • Metazoan||

    lol I work with an ENCODE collaborator, this is amusing to see it in pseudo-regular media. It's cool stuff.

  • Lucretio||

    I say its high time we break up these Soviet-style regulatory regions and let the free market decide whats best for our bodies' economy.

  • Metazoan||

    Interestingly it seems the evolution of life is the most free-market like thing imaginable, with no overriding guiding force at all, just...self-interested molecules?

  • Tulpa Doom||

    There's a lot of coercion in evolution.

  • T o n y||

    You know who else applied the supposed virtues of natural selection to the organization of society?

  • ||

    Progressives

  • Libertarian||

    Speaking of humans, here's the saddest damn thing that I saw on the Internet today.

    http://www.newyorker.com/online/blogs/photobooth/

  • Metazoan||

    holy shit.... thanks a lot

  • ||

    I dont care how much my body falls apart, as long as I can keep my mind intact. I would probably take a .45 and go for a long walk in the woods if I ever started suffering from dementia or Alzheimer's. Of course, with my luck, I would forget why I went for the walk.

  • Scarecrow Repair||

    I like it. Yes, it's sad that people wander off and look for a bus stop, and wait for none to arrive, but it's also a nice way to prevent them from actually getting lost while not restraining them with locked doors and guards. I had a relative who hated her home so much that she would leave without a destination just to get away, and it was pretty dangerous. This is a decent alternative in that respect.

  • MisterDamage||

    Wow, that's horrifyingly sad.

  • ||

    If there's no junk DNA, how do we explain Warty? This has thrown our whole STEVE SMITH/Warty classification scheme into doubt! There was a consensus, damn it! The science was settled!

  • ||

    Junk DNA, not Neanderthal DNA.

  • ||

    RNA, or "Rapeonucleic acid".

  • JW||

    Warty has always been, and always will be. He's nature's human coelacanth.

  • ||

    The cool thing about Warty is when you are doing research on him and ask for a seman sample so you can sequence. The man is a seman machine. In quantity, on target, on time better than Ron Jeremy. The phrase, "my cup runneth over" comes to mind.

  • Beefkins||

    I'm a semantic machine.

  • ||

    Warty is the pinnacle of evolution. A bad ass prodigal son whose ancestors killed and out competed all contenders.

    Of course everything alive today is the same....

  • George26||

    Its hard to forget about the democrats when they act to ban this stuff. Whenever someones happens on the very inconvient truth of the heritability of IQ, that person then becomes a "nazi" and the democrats then act to destroy thier career. When someone tries to put this knowledge for practical benefit, to feed more people, the democrats call to ban it. Becuase its better children in Africa starve than a scientist be allowed to harm "Gia."

  • Heroic Mulatto||

    "Gia" did enough harm to herself.

    Jus' sayin'

  • SKR||

    Cue GMO pearl clutching in 3 ... 2...

  • ||

    It could be that the difference between "junk" and "non-junk" is trickier than this article indicates. If you have a section of the genome that used to be useful, and then it became obsolete, and so it was turned off by a regulatory gene, then both the original sequence and the regulatory gene might be regarded as "junk".

    Sort of like a counterproductive government agency that is rendered ineffectual by a different government regulatory agency set up to ameliorate the original harm.

  • loving||

  • theDNAproblem||

    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.....ature=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.

  • AlisaIsbel||

    Nice post.I enjoy this post gorgeously with all of my friends.Really nice.thanks.

    ewald struggl

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