Scientists Discover How DNA Is Folded Within the Nucleus 152
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."
Origami? (Score:1)
How soon before we get folding-paper DNA model artwork?
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How soon before we get folding-paper DNA model artwork?
There was some in TFA.
tell me something a child couldn't figure out (Score:5, Funny)
Well OBVIOUSLY.
Re:tell me something a child couldn't figure out (Score:4, Interesting)
Yeah now. Seriously, while your answer is a bit flip, I did have that thought as well. All I know about DNA is the usual buzzword stuff - double helix, Crick and Watson, ACGT... etc. I never really thought about what it actually might look like.
But the diagram showing the tangled mess vs the "fractal" folding evoked a "duh" from me as well.
The trick is to be the first to prove a non-trivial "duh" fact.
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Then perhaps you should have chosen your Subject wording more carefully.
Re:tell me something a child couldn't figure out (Score:4, Insightful)
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AGCAGTACGCTGGTTG
That's the genetic encoding for "WHOOSH!"
No, this is: TGGCATCAACAATCTCAT! (well almost, there is no amino acid with O as its one letter symbol so I had to use Qs. So actually it spells WHQQSH: Tryptophan, Histidine, Glutamine, Glutamine, Serine, Histidine. Also I coverted the uracils to to thymines so as not to confuse you nice non-bioscience folk.)
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The first observation is that genes are actually stored in two locations.
This threw me off at first. It read like active genes have a backup stored somewhere in the inactive part. That is not the case =). We're not having and L1/2/3 cache in our genome.
Hilbert Curve (Score:3, Interesting)
Re:Hilbert Curve (Score:5, Funny)
So, life figured out a form of a Hilbert Curve [wikipedia.org] for storing data? Cool!
Now, if life could just figure out how to get the blinking numbers off of my VCR...
Re:Hilbert Curve (Score:4, Insightful)
It's very hard not to anthropomorphize natural selection. Even Richard Dawkins, who is about the last person in the world who would attribute evolution to some sort of intelligence, has pointed out many times how phenomenally hard it is to talk about the subject without constantly imputing goals and desires to the process.
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Hilbert peeked.
Obligatory (Score:5, Funny)
All your base-pair are belong to us.
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I wonder how you'd demonstrate prior art for that in court...
Actually no, I don't want to imagine it.
OH YEAH!!!! (Score:4, Funny)
When questioned about the research, Kool-Aid Man [google.com] could only sob dejectedly as his rival took the glory.
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i'm willing to bet ecto cooler was involved.
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Tang was only able to utter a "no comment."
So.... (Score:3, Interesting)
Re:So.... (Score:4, Interesting)
And it makes use of a primary cache. "That's hot."
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How long until some Akhibara electro-wizard overclocks your DNA with LN?
Fascinating (Score:5, Insightful)
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.
Re:Fascinating (Score:5, Insightful)
That is possible, non-coding DNA is already known to be a source of raw material for the evolution of functional genes and contains some gene regulatory regions. The concept that it retains other functions outside of direct coding of proteins isn't a new one. Also, few in the biological scientific community really calls "junk DNA" junk DNA any more because of the inaccuracy of doing so.
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Re:Fascinating (Score:5, Informative)
the "junk" DNA that we supposedly don't use
This idea seems to have become embedded in the pop-sci mythos nearly as firmly as the "we only use 10% of our brains" thing, and it's equally false. Absolutely everyone working in genetics these days understands that non-coding DNA has multiple biological functions.
In answer to your question: yes, it's entirely possible. I just really felt the need to get the above out of the way first.
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What /THE FUCK/ are the scare quotes for? Junk DNA is junk because it's content is useless, if it was there for structural purposes it would consist of the same base-pair repeated over and over. Instead junk DNA is compromised of a healthy dose of post-ad-hoc disabled vestigial genes and garbled ones. Since everything that affects your genome is in a sense part of your genotype it wouldn't be surprising if it is preserved but to suggest this DNA is not made of vestigial genes is, quite frankly, quite sick.
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Except that it isn't all junk. Yes there are vestigial genes and repeats such as Ala however, that does not mean that it serves no structural role. Some repeats especially GGG can distort the DNA coiling structure from the normal B form to other forms that are less useful (eg. Z).
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I don't mean that they are only vestigial and serve no structural purpose.
But rather that if they were placed there deliberately for structural purpose only it would be obvious and they would be made of vestigial genes.
They are junk, not "junk".
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You're acting as if we are really super sure about how they work and what purpose they serve. We have a very good idea of what is likely, but it's not as cut-and-dry as you make it sound.
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Since /. requires a car analogy in every discussion, here is one:
Engine, transmission and wheels are sufficient to move the car. However not many of us would buy a car that consists only of those three parts.
Re:Fascinating (Score:4, Insightful)
What /THE FUCK/ are the scare quotes for? Junk DNA is junk because it's content is useless,
You have no idea "What /THE FUCK/" you're talking about. Please stop spreading misinformation that even in the 70's, when the term "junk DNA" was coined, people had a vague idea probably wasn't right, and which we've known with certainty for 20+ years isn't true.
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I do, junk DNA, as well as other minerals and enzymes and pretty much anything that floats into the cytoplasm affects the functioning of DNA, they are as much part of your genotype as anything else, as should be expected, because the parts are there and interact, so the interaction must play a role in the expression of the phenotype.
Two thins are I know are, it wasn't placed there deliberately by some supernatural entity, it does not look even remotely designed, in fact we know exactly what it looks like, v
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I didn't see one scrap of "ID drone" in the OP. I saw someone who showed a surprising amount of open-mindedness and insight for someone carrying around a 30 year old misconception about seemingly unused section of DNA. The "scare quotes" were to imply that what we call "junk" wasn't "junk." Which of course is true even if he didn't know it. It's a tremendous and unjustified leap to go from that to assuming he's say "HAHA GOD DID IT EAT THAT SCIENCE." Do you assume that someone is anti-science any time
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And none of that is new to me the only news is that I'm running short on temper for creationists, probably caused by reading youtube comments.
Re:Fascinating (Score:5, Funny)
Could all the "junk" DNA that we supposedly don't use maybe have some sort of structural stabilization function?
That isn't "junk" DNA, that's God's comments inside the code you insensitive heretic!
Re:Fascinating (Score:5, Funny)
Real gods don't comment their code. It was hard to write, it should be hard to read.
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Corollary: If you write Perl even code that was easy to write is hard to read, making you look like a god. /x) and builtin variables ($_ FTW.)
Just use copious regexes (NEVER use
"Junk" = regulatory RNA (Score:2, Informative)
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
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good point -- though the DNA is non-coding, it's structural conformation alone can affect the expression of other factors in the coding DNA.
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considering how things interact with DNA, and how subtle changes in one place can cause unimaginably large changes in other unexpected places ("butterfly effect" of sorts) I believe very little of "junk" DNA is actually "junk", by the conceptual definition. Running over a pebble on the highway may seem irrelevant until you 're not allowed to move the steering wheel. Then see what a different outcome you get ten miles down the road when someone removes the pebble.
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The idea of "junk DNA" is waaayyy outdated. At least by a decade! It was the old error of arrogance, that led some scientists to believe, that when they could not find a use for it, it must be "junk". Until someone found it to be in heavy use, defining the details of what you become. (There was a very interesting article in the German version of the Scientific American [called "Spektrum der Wissenschaft"] about it, some years ago.)
It's what also caused people to believe that the spleen (the standing army he
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oh, _sure_ (Score:2)
Down the road:
... but, interestingly, this excision had a catastrophic effect on its progeny's ability to evolve ...
... or some other "oh, you didn't expect that" scenario, a là "Jurassic Park", a là "Frankenstein", a là "chaos", a là the incessantly repeating mythologem of man's hubris wherein some knowledge is mistaken for a holistic grasp or short-sightedness fails to promote a wariness about tangential effects, folks tread (or fly) incautiously, and then the shit hits the fan.
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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.
Re:An obvious question arises... (Score:5, Informative)
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'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.
Obligatory Evolution README (Score:3, Informative)
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 [oxfordjournals.org], 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
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Majic 102
How? (Score:2)
Very carefully.
Great (Score:3, Funny)
Now maybe Apple could apply this structure to my iPod earphones. They're _always_ getting tangled.
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The little white collar on 4Gen Shuffles doesn't go all the way up now, the controller gets in the way.
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Hey!!!
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Which is why they suck. In addition to the rubbery feel which tangles even worse than the iPhone/iPod headphones. I got one of these with my 3GS, and I immediately stole my wife's old pair of 2G headphones.
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Ever see a klein bottle? You have no idea the nasty tangles an extra dimension can get you into.
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Get yourself some real earphones then. They sound like crap anyway.
worlds smallest (Score:1)
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Well, proteins are getting folded into containers all the time. Check out ferritin [crystalprotein.com].
Then there are beta barrels [crystalprotein.com] ... [wikipedia.org], which act as kinds of containers.
Doc would listen to any kind of nonsense and change it for you into a kind of wisdom. His mind had no horizon and his sympathy had no warp.
... Unlike Doc Ricketts, you are not improving the situation; you are being petty and malicious.
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My take-away:
DNA looks like a rubik's cube made out of colored spaghetti.
I was reading all the responses to see if just this one comment got made. It's an excellent starting point to describe the function of the structure.
Both are designed so components can be far apart at one time, and after a manipulation (or X of them) are adjacent (or have some specific spatial relationship). Both require the manipulations follow a set of rules based on the structure. Most people know how the cube works, with its central rotating axis.
Imagine first that instead of that amazing little widget,
good job (Score:1)
Nice to see 2 familiar names in one article (Grosberg/Mirny)...
What about beads on a string? (Score:4, Interesting)
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 [wikipedia.org].
Is this information now obsolete?
Re:What about beads on a string? (Score:5, Informative)
No it's not, as I understand the paper, the important work was in determining the structure of the folding of heterochromatin. All other theories still apply, we just know more about the folding itself. You can see using electron microscopy that there are discrete locations for heterochromatin and euchromatin inside the nucleus, that theory still apples as well.
The "beads (histones) on a string (DNA)" architecture is one step above the double helix organizational order, this is also the form of more highly transcribed or "active" DNA (called euchromatin). From there, that string is then wrapped into a much more complex structure which significantly reduces the transcription levels of the mRNAs that this DNA encodes for (called heterochromatin).
The who field of epigenetics deals with regulating expression of DNA to cause cellular differentiation and changes in cells throughout their lives. One of those ways of regulation is the cell controlling which genes are found in euchromatin and which are found in heterochromatin for certain types of cells at a certain point in their life cycles.
The post below me about the Hilbert curves is also accurate, thermodynamics is at the heart of all DNA and protein folding.
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the folding referred to in that Wikipedia article is the folding that takes place when cells are about to divide. those X shapes you see under the microscope are two compressed copies of the gene. one copy goes into each cell. then the neat package is unzipped. the folding that is referred to in in this Slashdot post is how it is stored in the cell while it is actively in use.
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No it is more complete.
This describes genome order at scale larger than the nucleosome. Even the wikipedia article gets a bit vague as you go from the 10nm structures up to the 30nm structures. Notice the change in tone as the section changes from the nucleosome, which is very well described to the "here are a bunch of proposed models" in the next few paragraphs. There really isn't much to tell you where any two genes (separated along the length of a chromosome) should be relative to one-another in space
Not a coincidence (Score:2)
Anyone else wish they could read the publication? (Score:5, Insightful)
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Wow... (Score:2)
The guy who came up with this storage system was pretty damn smart. RAM with a swap drive, parity. Quite intelligent. Not at all random, if I may say so myself.
Re:Wow... (Score:5, Informative)
Actually, fractals generate arbitrarily complex structures with very simple rules (e.g. the Mandelbrot Set [wikipedia.org] - 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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TempY = zY^2
zY = c2 * zX * zY + cY
zX = X^2 - TempY + cX.
If the series of Z's should always stay
Close to Z and never trend away
That point is in the Mandelbrot Set
Make that point black. If the point "trends away" or gets too big, make it white.
I may b
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On the surface, it is very easy to attribute the complexity produced by natural selection as a non-random or directed process. Unfortunately, if you look at the number of failures which were required to come up with this arrangement (and the subsequent spread of the most fit type), it's still just as random as any other natural mutation process.
Unfortunately (Score:2)
You are ignorant about evolution. Anyone who says evolution is "random" doesn't know the first thing about evolution.
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And somebody who focuses on my using the word random doesn't understand the first thing about sarcasm. I'm quite aware of evolution; I just don't accept a certain premise upon which it is based. I also don't accept a certain premise about the opposing viewpoint.
However, I do think the issue itself is petty. It's a fundamentally useless controversy that does nothing to improve the quality of man; but at least reduces us to pointless bickering.
Re:Unfortunately (Score:4, Insightful)
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?
Re:Unfortunately vs ID-book recommendations (Score:1)
sheer marvel and scale
Both Sanford's "Genetic Entropy" and Behe's "The Edge of Evolution" contain back-of-the-envelope order-of-magnitude musings on "scale" related to the random-mutation-fantasy. David Swift's "Evolution Under the Microscope" stands out for repeatedly marveling over the "folding" issue, including the snip-and-rejoin magic needed to copy a helix. I mean I have repeatedly had the experience of spending tens of minutes unraveling a 50-meter stretch of 11-millimeter Edelrid perlon climbing rope, which is specif
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The environment is the subject. Saying it is diverse is a tautology. It still needs a damn good why to explain symbiotic and parasitic behaviour coexisting for instance, among the multitude of logical paradoxes in the natural realm.
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I am very disappointed... (Score:4, Funny)
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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Come on dude, it's no fun if someone spells it out.
This is not news. (Score:1)
This concept has been the subject of several review articles in the scientific journal Nature - as early as 2007to my knowledge.
More information (Score:3, Informative)
While it's not mentioned in the submitted article, I found this explanatory video helpful [youtube.com] in understanding the folding concepts.
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is it just me or (Score:2)
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Folding @ home? (Score:1)
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---
Genetic Engineering [feeddistiller.com] Feed @ Feed Distiller [feeddistiller.com]
nature is a computer? (Score:2)
machina ex Deus :-)
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what really?
you think nature is going to get lifted down on a crane and conveniently save the world for us in a lazy script-writer kind of way?
do you have a newsletter subscription on offer by any chance? :D
misleading (Score:2)
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.
"Cache" suggests a rapidly accessible copy, but that's not what's happening.
It's simply that active genes are accessible while inactive genes are inaccessible. That's not a new insight; that's been known for many years.
The paper does make valuable contributions, in that it describes the statistics of how genes relate to each other in 3D better than previously known
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"Cache" suggests a rapidly accessible copy, but that's not what's happening.
Only to computer geeks. :)
Most other uses of 'cache' imply that they are hidden out of the way, saved for a rainy day or guerrilla insurgency. :)