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Thread: Junk DNA, really junk or not ?

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    Question Junk DNA, really junk or not ?



    Between 80% and 98% of our genome is junk DNA - meaning that no function has been identified for it (yet). Does that mean that this DNA really does not have any function (anymore), or just that we haven't figured it out ?

    Few people outside the field of genetics know that our genome is affected by viruses, who have through hundreds of millions of years of evolution, slowly infiltrated our DNA sequence.

    A virus has the size of a small gene. Although it is not clear yet how it happens, a virus can place its genetic sequence inside our own, and stay there for subsequent generations, pretty much forever. In most cases it does not have any effect on the host, but occasionally a virus can intercalate itself inside a working gene and disable it or modify its function. This is one cause of evolution (the other being spontaneous mutations from generation to generation). In most cases it will kill the host, or leave it with a disability. But sometimes it will improve its health or confer it some new attribute, which will give it an evolutionary advantage.

    Junk DNA also consists of a large number of repeated copies of a short DNA or RNA sequence, which are apparently transcription mistakes that have accumulated over the generations. It has been estimated that 42% of the human genome is formed by such retrotransposons, as they are known, including 8% caused by Human Endogenous Retroviruses (HERVs). The latter are viruses that duplicate their genetic code within our genome just as a way of propagating themselves and ensuring their own survival. They are selfish genes par excellence, just caring about their own survivals, even if it is detrimental to the host.

    A small percentage of retrotransposons are copies of working DNA. The number of repeat copies of a DNA sequence within a gene can vary from person to person and has a direct effect on our health or behaviour. For instance, people with 7 or more copies of a specific 48-base pair sequence in the dopamine receptor D4 gene are more novelty-seeking and at higher susceptibility of developing ADHD than people with 2 to 6 copies. This is because having more copies increases the dopamine in one part of the brain.

    A third category of junk DNA is the disabled genes. We carry with us a lot of information about our ancestors. As apes, we don't have a tail anymore like other mammals or reptiles, but the gene for making a tail is still within our genome. The gene has just been deactivated. Theoretically, and ethical considerations aside, it would be possible to create humans with a tail by reactivating the gene by genetic engineering. There has been a lot of evolutionary changes from the bacteria to us, and therefore a lot of our DNA is also composed of old relics of this past.

    What I am wondering is if this Junk DNA is really all useless (or even detrimental), or if it is necessary for our proper genetic functioning. Scientists have tried deleting some junk DNA from mice, and they seemed to be just fine.

    But what would happen if all the junk clustering our genetic hard disk were to be cleaned up ? some working genes that had been separated by junk buffers might recombine and work differently, or stop working. For all we know, our body might need these retroviruses to fight other viruses, or prevent new insertions in "strategic parts" of our genome in future generations. The more junk there is, the less likely it will be that new HERV's will intercalate them inside working genes. If all our DNA is useful, then the slightest copying error or retrovirus contamination would have devastating effects on our offspring. So we might need that Junk DNA after all. On the other hand, it might also be possible to improve our health by removing a few noxious elements from our genome. Most important of all, some of the so-called Junk DNA might have vital functions that has not been identified yet.

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    In order to sabotage DNA constructive research, the demoralizing term "garbage DNA" was invented, their are people out there who want to keep the lid on everything that empowers individuals

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    Genetic Redundancy

    I am quite new to researching genetics and only learned of repeated genes just recently, but I figured it was just a "back-up" in case a vital code was compromised. It would be smart to have another copy of a gene that determines heart rate if that gene experienced a transcription error, etc. But then you would think that the most essential genes would have the most copies? Hmm, I guess not if it's a blind process.

    Is this possible?

    More of my uneducated thoughts: I cannot imagine any DNA being worthless. Even the tail gene would be useful if our environment shifted to one that made it useful, which you are well aware of. Active genes are only guaranteed to be useful in the present, in this lifetime, but DNA lives longer than our short stay here, it's just passing through. It only spends a tiny fraction of its "existence" in us, in these conditions. It's not "designed" just for us. Junk genes are potentials for a potential future.

    "Junk DNA" is a very ego-centric perspective.

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    To me, the "junk" concept does not make sense when applied to DNA.

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    Really not junk. Judge by yourself.

    New scientist : 'Junk' DNA gets credit for making us who we are

    Quote Originally Posted by New Scientist
    In recent years, researchers have recognised that non-coding DNA, which makes up about 98 per cent of the human genome, plays a critical role in determining whether genes are active or not and how much of a particular protein gets churned out.
    ...
    Together with Jan Korbel, a geneticist at the European Molecular Biology Laboratory in Heidelberg, Germany, Snyder led one of the teams. They found that transcription factors – proteins that attach to stretches of non-coding DNA and affect how nearby genes make proteins – act at very different locations on the genomes of different people.
    ...
    Snyder's team didn't study what effect these differences have, but he notes that points on the genome where transcription factor binding differed between people tended to be near genes implicated in schizophrenia, diabetes, rheumatoid arthritis and other ailments. He suggests, therefore, that these differences in transcription factor binding may affect disease risk.
    ...
    Kelly Frazer, a genomicist at the University of California, San Diego, says the new studies help explain why many common mutations linked to diseases are located so far from any gene. For instance, a certain mutation that increases the risk of heart attack by 60 per cent is not close to a gene.

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    Life is very efficient. I've always had a problem with so called junk DNA. Why would every organism invest so much energy and resources in keeping useless stuff in every cell? I'm glad we have the answer finally, and it's not junk!

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    It is not junk, it is the evolutionary trail. Our brain is half reptilian. We carry genes of a fish as we evolved from fish. When we are in the womb it is a liquid environment. I don't know if the umbilical cord supplies oxygen as well as food nutrients. Maybe the foetus uses gills to breathe in the womb. There have been incidents where babies with gills were operated on to remove the gills in the "weird news" section.

    It also means that we cannot regress as those mutations would be blocks. New genes or mutations might have to be made to adapt to the regressed environment such as after a nuclear war if we can survive the radiation. I think the blanks in the DNA are like a new book. Blocks are provided as we mutate. Like in the computer file system blocks may have a minimum size so genes may only be of such a size leaving some blanks. As we mutate more then I think the DNA would get longer.

    P.S. I just remembered doctors spank babies to make them breathe by crying so the foetus doesn't breathe in the womb.
    Last edited by oriental; 01-09-12 at 00:36.

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    The latest research from the the US National Human Genome Research Institute suggests that junk DNA isn't junk at all, but contains sections of DNA that are transcribed into RNA to form RNA switches (used to turn genes on or off, for instance stopping growth once the adult size has been reached, or starting puberty).

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    Yes, I read in the papers that maybe 80% is active. Look at a car though the frame and the seats are not active they are integral parts of the car.

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    If you know programming, then I'd assume coding proteins are the data. The rest is the source code. All we really have a hope to decipher is the former but the latter probably does most the work (though I'm sure, indeed, some of the instructions are no-ops or else have little effect).

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