(Not so) Junk DNA

Discussion in 'Biology & Genetics' started by Eflex tha Vybe Scientist, Oct 22, 2003.

  1. Eflex tha Vybe Scientist Registered Senior Member

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    It seems that our current ideas about DNA coding and gene expression are incomplete.

    DNA -> RNA -> Protein = only half the story!

    in fact, the entire concept of 'Junk DNA' might be a fallacy.

    Paul Samuel, remember our conversation about Dark Matter and Junk DNA?

    Well, it turns out that there are large sections of genes that are clearly functional even though they dont code for protein!
    Some code RNA, some might code for the behavoiur of cells.

    http://www.sciam.com/article.cfm?chanID=sa006&colID=1&articleID=000D9CB2-4F2D-1F7F-82D883414B7F0000
     
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  3. Eflex tha Vybe Scientist Registered Senior Member

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    BIOTECHNOLOGY

    The Unseen Genome: Gems among the Junk
    Just when scientists thought they had DNA almost figured out, they are discovering in chromosomes two vast, but largely hidden, layers of information that affect inheritance, development and disease
    By W. Wayt Gibbs

    About 20 years ago astronomers became convinced that distant galaxies were moving in ways that made no sense, given the laws of gravity and the fabric of celestial objects visible in the sky. Gradually they were forced to conclude that the universe is not as empty as it appears, that in fact it must be dominated by some dark kind of matter. Although no one knew what the stuff is made of or how it works, scientists could see from its effects that it is out there. The quest to understand dark matter (and more recently, dark energy) meant revising or replacing theories, but it reenergized astrophysics and cosmology.

    A similar revelation is now unfolding in molecular genetics. This year biologists celebrated the 50th anniversary of the discovery of the double helix, and the Human Genome Project announced its completion of a "final draft" of the DNA sequence for Homo sapiens. Scientists have clearly mastered DNA in the lab. Yet as they compare the DNA of distantly related species and look more closely at how chromosomes function in living cells, they are increasingly noticing effects that current theories cannot explain....continued at Scientific American Digital
     
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  5. ElectricFetus Sanity going, going, gone Valued Senior Member

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    About time someone mentioned that article (I do not post articles, I’m to shy) what the article is saying is that there could be a vast amount of genes in organisms that only produce RNA rather then mRNA to make proteins, in fact that article points to the possibility that there could be more of these RNA-only genes then protein producing genes, this is a revolutionary idea that goes against the central dogma that DNA must make RNA that makes Protein to be of relevancies. It has in fact been know for some time that such unorthodox genes existed but they were called exceptions rather then the norm, now evidence is mounting that these RNA-only genes are very common. It is going to take much more time to take full tally of these genes since they do not have the recognizable start and stop sequences of normal genes.

    The article also points to that RNA-only genes work by making RNA enzymes that actually catalyzes reactions on there own! Also make RNAs that work in gene activation and protein modulation, that these genes may be responsible for the much more analog nature of genes rather then simply being turned off/on. This is also may be a boost for RNA World theory that life started out only with RNA: if RNA is still used today for protein like and genetic tasks then it is not hard to postulated that RNA long ago was the means of genetic storage and functionality, with DNA coming later as more accurate and efficient storage medium and Proteins coming last as more variable enzymes and structural mediums (carbohydrates and lipids have a less necessary though still important place pre-biotic evolution).

    Even if RNA-only genes are more prevalent they would still not account for the majority of the human genome which is still most likely structural in task, this is because 90% of the human genome is made of constantly repeating sequences millions of times over with little to no variation, of the other 10% only 2% makes proteins that leaves a max of 8% for these RNA-only genes even so if a reasonable percentage of that 8% turns out to be RNA-only genes it would revolutionize genetics. Heck they have even linked genetic diseases to these things.

    By the way if the article used the similar revolution in astronomy of dark matter and dark energy why were these RNA-only genes not given the catch name of “Dark genes” that would have been so cool.
     
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  7. spuriousmonkey Banned Banned

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    na ja...doesn't sound very revolutionary. It is not like we haven't heard the presence of many RNA genes before. Or maybe it is just because there are some RNA people working in our institute.

    I didn't fall of my chair.

    not to mention that some genes actually can be spliced into 10.000s of different messengers all encoding different proteins. The viewpoint that genes are everything is really stale. Welcome to the new world.
     
  8. ElectricFetus Sanity going, going, gone Valued Senior Member

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    Its revolutionary to considers these genes as normal and even more common then protein sequencing genes.
     
  9. spuriousmonkey Banned Banned

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    just wait a few years. Don't get hyped up.

    The question is if they are all functional.
     
  10. ElectricFetus Sanity going, going, gone Valued Senior Member

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    thats right a tally should be done first.
     
  11. spuriousmonkey Banned Banned

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    And if this already floats your boat, what about the fact that some organisms have inevented new aminoacids and in fact have changed the genetic code.
     
  12. ElectricFetus Sanity going, going, gone Valued Senior Member

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    Ya I knew about that, but that’s not common,

    Please Register or Log in to view the hidden image!

    (noting the hypocrisy of that statement) at least its not possible in humans.

    Please Register or Log in to view the hidden image!

    Here is possibility of a huge amount of data that has been over looked in the human genome.
     
  13. CuriousGene Supreme Allied Commander Registered Senior Member

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    Just to clarify some numbers here for the sciforum readership . . .

    The human genome is more on the order of 50% repetitive. Even Celera's data show about ~37% repetition with the caveat that they have an underestimation. Also, clearly it's a misconception that most of the genome is junk. Media sources, like CNN and BBC, often report that only 3% of the human genome is useful and the rest is junk. The 3% is referring to only exons. But, I think it's clear that non-exonic components are quite functional. Examples of functional components outside of the 3% (and apparently living in the "junk" part of the genome) include transcription factor binding sites, introns, all types of regulatory sequences, and for all you RNA fans out there . . . there are even relatively newer classes of RNA known as micro RNA (small ~22 bps) sequences. The transcriptional terrority of polII genes alone to date (cause we haven't found them all yet) account for ~40% of the human genome.

    I think what is confusing is the role the repeat component of the human genome plays. There are repeat sequences inside genic content that would preclude one from arguing that there is just "junk" in portions of the genome that contain repeats. Also of importance is the potential role that these repeat sequences themselves play in the evolution of our genome. As one of many examples of possible repeat sequence function, there is strong evidence of a repeat-driven expansion of the human genome. In addition, Alu repeats (the most ubiqitous repeat class in our human genome) have been the focus of many papers regarding their possible function . . . one of which is the linking of Alu sequences to the origin and expansion of segmental duplications which has certainly shaped our nuclear genome. Repeats in general have helped shape our genome by allowing for a dynamic medium for our genome to evolve through. Both retroposons and transposons have facilitated rearrangements, translocations, deletions, insertions, and duplications within our human genome.

    When people say "junk", I wonder if they actually think they would not be any different without 97% of their own nuclear genome.
     
  14. spuriousmonkey Banned Banned

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    how anthropomorphic of you.
     
  15. ElectricFetus Sanity going, going, gone Valued Senior Member

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    spuriousmonkey,

    Really how so?
     
  16. Eflex tha Vybe Scientist Registered Senior Member

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    thanks for the clarification.
    But I have spoken with many a Biologist that refers to the "non-coding" sections as Junk.

    I am of the opinion that there is no such thing as "Junk DNA".
     
  17. Eflex tha Vybe Scientist Registered Senior Member

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  18. BigBlueHead Great Tealnoggin! Registered Senior Member

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    Being a Biologist doesn't make you a Molecular Biologist... the people you talked to may get their information about genetics from the news like everybody else.

    Even pretty respectable periodicals (Science, Nature &c.) still have a bit of a problem with their reporting style sometimes, and if a person's field of biological expertise is Animal Structure and Anatomy or something like that, it's not a good idea to assume that they're also well versed in genetics.

    After all... most of the software engineers I knew barely passed first year Calculus... people don't always bother to learn things that they don't like.
     
  19. Eflex tha Vybe Scientist Registered Senior Member

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    'JUNK' DNA - lol

    http://vitals.nbcnews.com/_news/201...project-shows-us-living-beyond-our-genes?lite
    the stretches of DNA that we call genes are only a very small piece of what makes the body work. Much more important is the stuff in between the genes – stuff once dismissed as “junk DNA”. It turns out that junk DNA is what is in control, they report in the series of papers in the journals Nature, Science and elsewhere.
     
  20. Eflex tha Vybe Scientist Registered Senior Member

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  21. Balerion Banned Banned

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    Eflex tha Vybe Scientist?

    Now I wish I still had my old screen name.
     
  22. Eflex tha Vybe Scientist Registered Senior Member

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    lol
    What is your old screen name?
     
  23. ElectricFetus Sanity going, going, gone Valued Senior Member

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    Oh unholy thread necromancy!

    I'm still surprised at the 80% activity figure though, there own papers can only verified that 5-9% of the non-coding DNA has vital regulatory functions via conserve sequences mapping between us and other mammals. At comes to ~10% of the genome, not 80%, so where do they claim the other other 70% supposedly does?
     

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