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RNA May 'Run' Genetic Coding
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)"
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
http://www.sciencedaily.com/releases/2005/09/05090 6081607.htm
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.
There is much more to that already.
b s/nature03315.html
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/a
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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...