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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."
How soon before we get folding-paper DNA model artwork?
Knowledge is how to play a game, intelligence is how to win, wisdom is knowing what game to play.
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!
"Be prepared, son. That's my motto. Be prepared." --Joe Hallenbeck
All your base-pair are belong to us.
Knowledge is how to play a game, intelligence is how to win, wisdom is knowing what game to play.
When questioned about the research, Kool-Aid Man could only sob dejectedly as his rival took the glory.
"Trolls they were, but filled with the evil will of their master: a fell race..." -- J.R.R. Tolkien on Olog-hai
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.
how exactly did the DNA get folded in this manner?
How is DNA folded into the nucleus of a cell without being tangled?
Very carefully.
One of our competitors trademarked the term "hypothesis". From now on, we will call them "boneheaded ideas".
Now maybe Apple could apply this structure to my iPod earphones. They're _always_ getting tangled.
Once I was a four stone apology. Now I am two separate gorillas.
origami. I hope they can fold my DNA into crane... or a box.
Comment removed based on user account deletion
So, was this project a huge success?
Cake for everyone. It's not a lie.
This is cool and all, but we've known about the tiered system of DNA storage (the "first observation") for a while now. Really, the journalist here could have done better.
And as for the second observation, which depended on their cool new mapping method (barely mentioned!), it's not an actual fractal. It's instead a more tightly folded, vaguely fractal-esque glob of protein and DNA that keeps nearby sections of DNA close together in the glob, compared to the more tangled equilibrium glob model.
Article abstract:
We describe Hi-C, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. We constructed spatial proximity maps of the human genome with Hi-C at a resolution of 1 megabase. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.
Nice to see 2 familiar names in one article (Grosberg/Mirny)...
I do not believe in karma. "Funny"=-6. Do good and forbid evil. Yours, Oft-Offtopic Flamebaiting Troll.
Who cares? Whats far more important is when Meatloaf's new scheduler is going to make it into the Linux kernel. I for one am really excited about it.
Yes, but does it run Linux on the new organic-DNA-based processors due out any day from the Monsanto gene-patent farm?
Knowledge is how to play a game, intelligence is how to win, wisdom is knowing what game to play.
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?
It is a solemn thought: dead, the noblest man's meat is inferior to pork.
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.
It looks like a Hilbert space filling curve to me.
This article has a picture that shows the location of the fractal globule.
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.
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.
What those who want activist courts fear is rule by the people.
If humans had a task to engineer a solution for this task, how would we do it?
I patent this new invention! You all owe me money or you may not reproduce!
I guess I'll have to wait the 12 months as per the NIH policy.
You are ignorant about evolution. Anyone who says evolution is "random" doesn't know the first thing about evolution.
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.
When information is power, privacy is freedom.
This concept has been the subject of several review articles in the scientific journal Nature - as early as 2007to my knowledge.
I subscribe to Science as a AAAS member, and you can always go to a library for this popular journal.
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.
"Empathise with stupidity, and you're halfway to thinking like an idiot." - Iain M. Banks
Great.. Thats just great. I suppose everyone is gonna want to have their _own_ DNA now.
While it's not mentioned in the submitted article, I found this explanatory video helpful in understanding the folding concepts.
#DeleteChrome
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 specifically designed to be easy-to-handle. The idea of your genome getting tied up into knots, I mean really you DO want to ask how it possibly AVOIDS getting tied up in knots !
does the wording of the post sound like a computer geek trying to explain science. So you have this dense storage medium and the bus that runs through it to compile components that ultimately get displayed as proteins.
With all these mentions of folding, has this research taken advantage of the Folding@home project? I'm just curious.
machina ex Deus :-)
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, collections of cube components were allowed to slide between other such collections and the central axis, IFF the one sliding under and the one being slid under matched. It complicates the familiar rules of the cube a bit but allows some much quicker solutions.
Once you grasp that, extend it by allowing the same sort of sliding-between to occur between outside surface and the set allowed to slide between from the first rule set change. And also one allowed to occur between that first slider-under and the central axis. Now you've got, going inside from the outside, the outside face components, a second generation set that slides under it, the first gen set, and the central axis.
This can be extended through as many iterations as necessary to get all the components to come into all the possible configurations. But is doesn't have to be because not all configurations are desired, only those that allow match-ups of specific components of interest. That constraint on the rules makes them less complex, which is good, but less flexible, which could be bad.
Except it's not bad, because although the entire structure is built (to reply here to the response just below) just like beads on a string, you are armed with (1) perfect knowledge of all the desired matches that are needed to occur as well as of (2) all the layers and pass-betweens needed in order to bring about all the desired configurations. Furthermore, you are (3) being allowed to preload the beads on the string in any configuration in order to make the matching process, including intermediate steps, as efficient as possible.
To compare it back to the cube, it is as if you are going to be required to solve it, but you'll know that the starting state will be 'solved' as well as what subset of the rules will be used in the scrambling, meaning those are all you'll need to re-solve it.
As to why this comes out fractal: you have knowledge/control over the design in terms of matches that need to happen, all the slide-through rules allowed, and over the pre-loading of the beads to make a specific design as efficient as possible. You can set it up any way you need to in order to make the design process as well as the decoding process efficient, but once done it can't be changed. Since the structure is one of beads on a string the underlying configuration is linear. Because you can pick and choose the rules governing that linear structure in order to make it efficient, you are optimizing a set of interdependent rules. And because once set they can't be changed, you are developing an invariant rule set.
You have three invariant and interdependent linear rules. At each step of the solution/folding process, it can be describe as:
X in terms of Y and Z
Y in terms of X and Z
Z in terms of X and Y
simultaneously (ie. describing its state)
The next step in folding/solving will proceed the same way, all three set up and carried out simultaneously. At each step between fully folded/scrambled and fully matched/solved, the structure can be describes as a state of being closer or farther from being properly folded/solved (ie. farther = more scrambled than, as opposed to X steps from), while keeping in mind that some intermediate steps required to produce the desired end result are actually farther from the desired state than the start state or other intermediate states.
Now, if you graph that scrambled
"I may be synthetic, but I'm not stupid." -- Bishop 341-B
"the information density in the nucleus is trillions of times higher than on a computer chip"
That mother nature actually manages to keep each one of the billions of 2-meter strands of DNA in a person's body untangled is a little beyond me. I mean, I've got a couple degrees, and I still routinely spend 20 minutes at a time untangling guitar chords. And I don't even want to think about the mess that lives under my computer desks... Not to mention, have you ever been on a sailboat? Mother of god!
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.
This is yet another triumph of Neo-Darwinian evolution! Keep in mind that while it appears designed, you must keep telling yourself that it evolved, guided only by natural selection. Its no different really when you go to Best Buy to select a new computer. Imagine that you are "Mother Nature" doing the selection of the most fit, and you come across a computer with a cache, and a computer without a cache. Naturally, you are going to pick the one with the cache because its going to give you much better video. Well, that's exactly how this came about. Isn't it obvious? I mean, if you can't see it, then you are obviously ignorant. And don't start asking questions about where the cache came from in the first place!