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Scientists Discover How DNA Is Folded Within the Nucleus
mikael writes "Sciencedaily.com is reporting that scientists have discovered how DNA is folded within the nucleus of a cell such that active genes remain accessible without becoming tangled. The first observation is that genes are actually stored in two locations. The first location acts as a cache where all active genes are kept. The second location is a denser storage area where inactive genes are kept. The second observation is that all genes are stored as fractal globules, which allows genes that are used together to be adjacent to each other when folded, even though they may be far apart when unfolded."
The first observation is that genes are actually stored in two locations. The first location acts as a cache where all active genes are kept. The second location is a denser storage area where inactive genes are kept. The second observation is that all genes are stored as fractal globules, which allows genes that are used together to be adjacent to each other when folded, even though they may be far apart when unfolded.
Well OBVIOUSLY.
So, life figured out a form of a Hilbert Curve for storing data? Cool!
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So, what you're telling me, is that DNA naturally defragments itself, in order to be usable even in an archived state?
Could all the "junk" DNA that we supposedly don't use maybe have some sort of structural stabilization function? It wouldn't actively code for any proteins but the coding structure itself might allow it to make these shapes and/or allow the globule to move without causing knots in the structure.
Now maybe Apple could apply this structure to my iPod earphones. They're _always_ getting tangled.
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Ok, I'll bite. I'll start by positing that this kind of structure is more efficient or accurate but not 100% necissary to life. An assumption, granted but with a bit of research it should be possible to confirm or deny that hypothesis.
Given that it isn't necissary and is quite complex primitive life probably didn't have it, but due to the fact that is is more efficient or accurate it became more and more common in the gene pool. You know, the exact same way that any feature evolves.
It's already been known for a few years now that the "junk" scales directly with complexity of the organism - unlike number of genes, which does not. It's becoming increasingly apparent that huge numbers of "junk" sections of DNA are actually transcribed to RNA, and play essential roles in regulating what gets made into protein.
The new hypothesis is that RNA is the computational engine of the cell, allowing it to rapidly process information and react appropriately, and the non-protein-coding "junk" sections are what it uses to do this.
There's a guy called John Mattick from the University of Queensland who has done a lot of really exciting work in this area, and gives a fantastic talk on the subject - here's an abstract for a version of it. Sample quote:
the extent of non-protein-coding DNA increases with increasing complexity, reaching 98.8% in humans, suggesting that much of the information required to program development may reside in these sequences. Moreover it is now evident the majority of the mammalian genome is transcribed, mainly into non-protein-coding RNAs (ncRNAs), and that there are tens if not hundreds of thousands of long and short RNAs in mammals that show specific expression patterns and subcellular locations. Our studies indicate that these RNAs form a massive hidden network of regulatory information that regulates epigenetic processes and directs the precise patterns of gene expression during growth and development.
Using the argument that cells are RNA machines, there is most likely no junk whatsoever in the human genome.
I'm confused, here. I'm certainly no biology expert, but I have taken a few courses, one of which the prof seemed to describe exactly how DNA folds. Indeed, it's spelled out in detail on this Wikipedia page on chromatin.
Is this information now obsolete?
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Anyone else wish they could read the actual publication? It's sad considering this is partly taxpayer funded and given the NIH's and Harvard's push toward open access that the authors didn't choose a more accessible journal for such a groundbreaking piece of work.
Actually, fractals generate arbitrarily complex structures with very simple rules (e.g. the Mandelbrot Set - take a complex number, square it, add the original number, repeat.) That's pretty much exactly the kind of structure you'd expect an evolutionary process to come up with. If I may say so myself.
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I would guess that the development of this sort of fractal packing was a watershed moment in the development of eukaryotic life, but the process itself can be logically seen as an extension of existing processes. Most bacteria, which lack a nucleus, arrange their DNA in a simple circle.
This has advantages: the entire genome is always accessible for transcription and replication, there aren't telomeres to deal with, and it requires less maintenance. There are disadvantages: if every gene is accessible to the cytoplasm, you have actively keep the 99% you aren't currently using shut off, which is why bacteria use the operon system, and a big circular strand floating around is liable to tie itself in an awful knot. Bacteria have the equipment to fix small topologically issues in their genome, but overall, bacterial genomes are limited in their potential size. Some more complex bacteria have found a partial solution: they draw folds of their circular genome around proteins, to make a single circle more manageable as a group of pinched off loops. So you can see that there's an intermediate stage between "circle" and "our DNA has Hausdorff dimension 3."
Of course, if you're going to head down the road of DNA folding, you would really benefit from a plan. The beauty of fractals, and a reason they are found so often in the natural world, is that very complex behavior can come from the repeated iteration of very simple rules. Your cells don't need to understand Hilbert curves; all they need is a protein complex that grabs a strand of DNA, then puts a short, specific sequence of folds in it. As that happens along the entire strand, you make a space filling curve that would impress a mathematician.
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It seems to me that Benoit Mandelbrot's discovery of fractal math is at least as important as Buckminster Fuller's obsession with geodesics. If Fuller got "Bucky Balls," I think fractal globules really ought to be called Benoit Balls.
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It's all fractal. All the turtles. All the way down.
So look at the large scale, and it is clearly evident that the DNA folding is simply a self-similar scaling of the Flying Spaghetti Monster.
Will
Anyone with an interest in evolution and what modern studies of evolution are all about really should read this:
Darwinian Evolution in the light of Genomics, EV Koonin, Nucleic Acids Research 2009 37(4):1011-1034; doi:10.1093/nar/gkp089
Does it directly answer your question? No, it does not. However it will give you the framework necessary for understanding answers when they come along. And it is a good overview of where we are in the studies of evolution, what has been refuted in older theories, and what directions future studies will be taking.
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To which premise do you refer? That it is carried out by the passing of genetic information to offspring, or that it is driven by competitively succesful adaption? I'm not sure of any other premises, and while the first seems undeniable (the 'how') the second is more questionable (the 'why'). I'm a bit hesitant that we even have the first clue why, and are barking up the wrong tree entirely. The sheer marvel and scale of the extrodinarily diverse forms that life takes needs a damn good 'why', 'natural selection' just passes the buck to the invisible hand of mother nature. It's not a petty question as to why evolution happens, indeed most of the answers explored so far have given us great insight into all life on Earth. So without invoking omnipotent beings (which evolution doesn't even speak of anyway) or pointlessly bickering could I politely enquire what premise troubles you?
While it's not mentioned in the submitted article, I found this explanatory video helpful in understanding the folding concepts.
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