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RNA May 'Run' Genetic Coding

Posted by Zonk on from the new-boss-same-as-the-old-boss dept.

leonbrooks writes "First a Stanford Medicine Magazine article speaks about RNA 'produced by plants that turn genes on and off', and now a Science Magazine issue says 'For a long time, RNA has lived in the shadow of its more famous chemical cousin DNA and of the proteins that supposedly took over RNA's functions in the transition from the 'RNA world' to the modern one. The shadow cast has been so deep that a whole universe [of RNA] has remained hidden from view, until recently' and speaks of 'an order of magnitude more transcripts than genes', suggesting that more actual coding is done through RNA than DNA. Is everything we know about genetics off-base? (no pun intended)"

20 of 168 comments (clear)

  1. Science by Mozk · · Score: 5, Insightful

    This is how science evolves. One theory revises another. At least they're willing to say they they were wrong, unlike hundreds of years ago.

    --
    No existe.
    1. Re:Science by QuantumG · · Score: 3, Insightful

      There's nothing to be wrong about here. It's simply a question of focus. It took a long time to get to the point we are with genomics, now we can look at proteins and transcription control via RNA and actually discover what is going on.

      --
      How we know is more important than what we know.
    2. Re:Science by Salis · · Score: 4, Informative

      It'll more likely be translational control via RNA.

      RNA can quickly hybridize with regulatory regions of mRNA and change their translation rate.

      And these RNA transcripts can be very small, but still regulate the translation of many genes. It'll be a while until the function of all of these RNA's are understood.

      --
      Favorite /. tagline: "On the eighth day, God created FORTRAN." And it was good.
    3. Re:Science by rve · · Score: 3, Funny

      On the contrary, whenever a scientific theory is proven wrong or incomplete, that just proves that all of science is wrong and the earth was created in 6 days, 6000 years ago.

    4. Re:Science by Tim+C · · Score: 3, Insightful

      Thats not entirely true - scientists have held their hands up and said "we got it wrong" since people started doing science. Likewise, there have always been people who - for whatever reason - have not done so, even when presented with evidence proving it.

      Often it's because it's incredibly hard to admit even to yourself that the thing you've spent most of your working life on so far is wrong, that you've "wasted" all that time. Also, don't forget that there have been times when theory Y has replaced theory X, only for it to turn out that theory X is *also* right (I'm thinking especially of wave/particle duality - for a long time we "knew" that light was made of particles, then we "knew" that it was actually made of waves, now we "know" better)

      --
      It's official. Most of you are morons.
    5. Re:Science by Anonymous Coward · · Score: 5, Informative

      There is much more to that already.

      It is widely known that small RNAs can regulate translation of mRNAs by binding to them in the context of specialized protein complexes (e.g. RISC) but they can also target these same mRNAs for degradation or impair their production in the first place by blocking transcription.

      I believe that you are refering to microRNAs (although there are many other types).
      MicroRNAs are commonly thought to control expression of cognate mRNAs only by inhibiting their translation but that is far from being the actual case. In fact, while this may be a common trend among the characterized microRNAs from animals, most plant microRNAs act by degrading the target mRNAs. In addition, a recent letter to Nature pointed that many microRNA targets in animals may be degraded in the process: http://www.nature.com/nature/journal/v433/n7027/ab s/nature03315.html
      (sorry, subscription only)

      Furthermore, there is clear evidence from plant and yeast species that small RNA molecules can regulate the structure of chromatin (the bundles of DNA and histone proteins which constitute the chromosomes themselves). By regulating the status of chromatin you can also regulate the expression of the underlying genes. It is still not clear if the same happens in animal cells...but it is possible (and many say likely).

      This adds to three different levels at which small RNA molecules can regulate the information flow from DNA->RNA->protein and we are just scratching the surface since most of these small RNAs and their targets are still being discovered (by the hundreds).

      The funny thing is that until 1998-99 these small molecules (20-40 nucleotide long) were simply dismissed as junk...

  2. no pun intended by Anonymous Coward · · Score: 4, Funny

    All your base are belong to RNA.

  3. Too Bad... by xski · · Score: 5, Funny

    Is everything we know about genetics off-base? (no pun intended)

    I thought it was a great pun.

  4. I suspect so but didnt know for sure by taj · · Score: 4, Interesting



    RNA is the hardest to work with in the laboratory. It just fall to pieces. When I was working with DNA/RNA/protien it was just really hard to work with RNA.

    so DNA->RNA->Protein

    We could work with DNA we could work with most protiens. RNA? no way. well sortof but.. no way.

    So DNA and Protein do play major rolls no doubt. but we could not get an angle on the RNA. 1990's tech.

    1. Re:I suspect so but didnt know for sure by mlush · · Score: 5, Informative

      RNA is the hardest to work with in the laboratory. It just fall to pieces. When I was working with DNA/RNA/protien it was just really hard to work with RNA.

      I'd disagree, sure RNA is fragile and falls apart at the drop of an RNAse (1), but its chemically uniform, one batch is pretty much like the next and there are plenty of commercial protocols and reagents for manipulating it.

      Working with RNA really a matter of good technique (paranoid levels of cleanness and make sure all reagents are free of RNAse). If I had a sample of RNA that coded myosin, a sample that coded for pepsin and a sample of total RNA (all the different RNA molecules in a cell). I can use exactly the same methods to purify and study them.

      Protein on the other hand is a pit of horrors, the thing is that every protein is different, what works with one protein will completly degrade another, some proteins are so unstable that they degrade with time even under perfect conditions, some are so rare that there may only be 2-3 molecules in a cell. With RNA there are thousands of labs and really BIG money working on essentially the same molecule, with protein you may be the only person ever to study it

      (1) RNAse is the bugbear of RNA work, its a normal part of every cell and its job it to break up RNA (which it does very well). When its in the cell its kept under close control, however if the cell is broken up (to extract RNA for example) the control is broken and it eats any RNA it can find. When prepareing RNA the first step it to break up the cells/tissue and inactivate the RNAse without damaging the RNA (not too hard there a strong solution of salts it used). The trouble is that RNAse is really really stable, you can spit in a testtube boil it for 10 minutes and the only enzyme still active is RNAse. When the salts are removed and RNA extracted, any RNAse contaminant will reassemble and eat the RNA.

    2. Re:I suspect so but didnt know for sure by TCQuad · · Score: 3, Interesting

      RNA breaks down without RNase. Physically, RNA is much less stable than DNA purely becuase it is not double stranded (in most cases).

      Actually, the 2'-hydroxyl (the difference between deoxyribonucleic acid and ribonucleic acid) is a more significant problem. DNA is not hydrolyzable because it lacks any remaining hyroxyl groups (they're busy making the backbone bonds between the bases), while the sugar backbone in RNA can be hydrolyzed by base (base like NaOH, not like A, C, G, T, U...), cutting the single RNA into two pieces.

  5. oh good lord by CupBeEmpty · · Score: 5, Insightful

    ok as someone that works in this field let me say this:

    RNAi is a very useful tool, but this is definitely several years behind the curve. RNA has been shown to regulate much more than previously thought. However talk about "the secret world of RNA" is pretty much like claiming that there is a "secret world of open source software." Neither one is very secret or very new.

    The biggest contention I have is this quote from the article: "This knack of completely eliminating a protein makes RNAi a valuable research tool." This is wrong, because RNAi does not work like this at all. This is actually one of the drawbacks to using RNAi to eliminate proteins. It does not eliminate, it reduces. To get rid of a certain protein, the classic method is to completely remove the DNA that codes that protein from the organism studied. This is referred to as a "knock out" because the organism has no ability to make that proteind from the removed DNA. RNAi however, provides only a "knock down" because the DNA is still there and no matter how much RNAi is used there is still some expression of the protein. Also, many RNAi protocols are transient supressors not permanent knock outs of protein.

    So basically this is an exciting new field but don't necessarily believe all the hype because this is no miracle answer. The article is good, but oversimplified.

  6. Short Interfering RNAs by Anonymous Coward · · Score: 3, Informative

    The article is referring to short interfering RNAs (aka micro RNAs), which exert their effect post-transcriptionally (i.e., they are not involved in 'coding' as the summary suggests, but rather in suppressing the expression of 'coding' mRNAs that have already been produced via transcription).

    It is not that what was previously known was 'wrong'; RNAi is just an additional (and important) layer in the regulation of gene expression beyond what was previously recognized.

  7. C'mon by Otter · · Score: 4, Insightful
    Is everything we know about genetics off-base?

    It's worth noting that the field of "genetics" precedes even the identification of DNA and RNA. It may be that what we now know about gene regulation is wildly incomplete (although even that is unlikely, although possible) but Mendelian genetics is completely agnostic as to whether "genes" are protein-coding or not.

    --
    What I'm listening to now on Pandora...
  8. No subscription to Science mag online? No prob... by Veenix · · Score: 3, Informative
    For those of you without a subscription to Science magazine online, here's an amusing solution - Coral Cache, since NYU has basically a subscription to all academic publications :)

    http://www.sciencemag.org.nyud.net:8090/cgi/conten t/summary/309/5740/1507?rbfvrToken=bba41c737e9d32e 852952029f4e32998530ff0d1

  9. Re:no pun? by djupedal · · Score: 3, Informative

    Puns, as anyone who understands the concept of this particular type of humor knows, generally fall into two categories: obvious and subtle.

    In the case of an obvious pun, the tag line has come to be expected, and functions as a means of self-effacement, which is a respected attribute in many cultures. "Oh, wow...look...I just made a funny! I hope everyone appreciates the serendipitous nature and doesn't think I wrote the entire paragraph just for that purpose...? Honestly, it was just luck!"

    Then of course, you have the punster who, fearing that their efforts at humor will go unappreciated, use such a tag to help focus/force attention on their autoring prowess, and thereby increase the overall audience. Leave no laughter behind...

    In the case of 'i hate when ppl say...', most agree that this is simply an act of jealousy, where the childish hope is a dig will get them part of the (positive) attention as well, when, in fact, it usually warrants little more than pity.

    In those cultures where punning is a part of daily life, intended or not, such gestures should be encouraged, not derided, since they help us to identify with others, while allowing us to show our individual ability to give and take - aka share.

    Try living in a culture where the pun is non-existent. Conversations become boring rather quickly, and you have to find less elegant means of making a point. Some learn alternate means of expression, and some find it just too much work, and then become nothing but spectators. Personally, I find being able to use a pun means being able to craft better conversations, and I hate it when people don't 'get it'...

  10. Damn registration. Here is recent similar article by zymano · · Score: 4, Informative

    http://www.sciencedaily.com/releases/2005/09/05090 6081607.htm

  11. Actually... by Zouden · · Score: 3, Informative

    It's Kary Mullis, and he made an absolute fortune from PCR. The patent on Taq-pol is one of the most valuable patents ever.

    Secondly, you should be modded down for copy-and-pasting that diatribe against HIV/AIDS which is quite off topic.

    And while Kary Mullis made a brilliant discovery (PCR) he came up with it while he was stoned (no joke). This explains a lot of his unconventional theories...

    --
    "A week in the lab saves an hour in the library"
  12. Re:mRNA is fascinating stuff... by RyanFenton · · Score: 4, Interesting

    Nah - iRNA is a subset of mRNA (see your link), which is all a subset of RNA. mRNA is so fascinating to me because of the ranges of messages that can be sent, and what all those interactions really mean. So far it seems that various kinds of mRNA, not just iRNA can be used ultimately to manipulate DNA on and off to help us see what the whole of DNA ultimately can functionally mean.

    Again, I'm just a layman on the issues - and find it deeply fascinating in terms of the pure science of it.

    Ryan Fenton

  13. Role of RNA in Early stages of Evolution of Life by Aeternal · · Score: 3, Informative

    Commentators in this thread seem to have missed one of the main implications of the quoted article (this implication is not a new one anyway): Early organisms were functionally organised, and genetically coded for, by RNAs. DNA and proteins, including the catalytic functions of enzymes, came later. See the following, for example: "1: Nature. 2002 Jul 11;418(6894):214-21. Related Articles, Links The antiquity of RNA-based evolution. Joyce GF. Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. gjoyce@scripps.edu All life that is known to exist on Earth today and all life for which there is evidence in the geological record seems to be of the same form--one based on DNA genomes and protein enzymes. Yet there are strong reasons to conclude that DNA- and protein-based life was preceded by a simpler life form based primarily on RNA. This earlier era is referred to as the 'RNA world', during which the genetic information resided in the sequence of RNA molecules and the phenotype derived from the catalytic properties of RNA."