Beta
×

Welcome to the Slashdot Beta site -- learn more here. Use the link in the footer or click here to return to the Classic version of Slashdot.

Thank you!

Before you choose to head back to the Classic look of the site, we'd appreciate it if you share your thoughts on the Beta; your feedback is what drives our ongoing development.

Beta is different and we value you taking the time to try it out. Please take a look at the changes we've made in Beta and  learn more about it. Thanks for reading, and for making the site better!

Scientists Discover How DNA Is Folded Within the Nucleus

timothy posted more than 4 years ago | from the very-small-laundries dept.

Biotech 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."

cancel ×

152 comments

Sorry! There are no comments related to the filter you selected.

Yay (-1, Offtopic)

TheCount22 (952106) | more than 4 years ago | (#29763361)

Sweet I am the first to post.

Unfortunately I have nothing to say....

Re:Yay (-1, Offtopic)

mhajicek (1582795) | more than 4 years ago | (#29763409)

I could have beat you to it, but I had nothing to say so I didn't.

Re:Yay (-1, Offtopic)

Yvan256 (722131) | more than 4 years ago | (#29765179)

Hey, it's George...

I got nothing to say.

(beep)

Origami? (1)

davidwr (791652) | more than 4 years ago | (#29763363)

How soon before we get folding-paper DNA model artwork?

Re:Origami? (1)

mhajicek (1582795) | more than 4 years ago | (#29763395)

How soon before we get folding-paper DNA model artwork?

There was some in TFA.

Far more important (-1, Offtopic)

Anonymous Coward | more than 4 years ago | (#29763749)

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 (0, Troll)

davidwr (791652) | more than 4 years ago | (#29764095)

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?

Re:Origami? (0)

Anonymous Coward | more than 4 years ago | (#29764043)

It's been done: http://www.sciencemag.org/cgi/content/abstract/325/5941/725 , but with real DNA folded into shapes.

tell me something a child couldn't figure out (5, Funny)

nomadic (141991) | more than 4 years ago | (#29763407)

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.

Re:tell me something a child couldn't figure out (4, Interesting)

NotQuiteReal (608241) | more than 4 years ago | (#29763501)

Well OBVIOUSLY

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.

Re:tell me something a child couldn't figure out (2, Insightful)

nomadic (141991) | more than 4 years ago | (#29763591)

I wasn't trying to be flip, I was trying to be sarcastically funny. This wasn't obvious to me at all, and sounded kind of complicated (but then again I'm not a biologist/geneticist/whatever).

Re:tell me something a child couldn't figure out (0, Flamebait)

NotQuiteReal (608241) | more than 4 years ago | (#29763961)

I wasn't trying to be flip

Then perhaps you should have chosen your Subject wording more carefully.

Re:tell me something a child couldn't figure out (3, Insightful)

nomadic (141991) | more than 4 years ago | (#29763999)

Nah, I don't think so. It fits in with the sarcastic thing.

Re:tell me something a child couldn't figure out (0, Troll)

bheekling (976077) | more than 4 years ago | (#29764557)

You got modded troll. Still think so?

Re:tell me something a child couldn't figure out (0)

Anonymous Coward | more than 4 years ago | (#29765153)

AGCAGTACGCTGGTTG

That's the genetic encoding for "WHOOSH!"

Hilbert Curve (3, Interesting)

ground.zero.612 (1563557) | more than 4 years ago | (#29763423)

So, life figured out a form of a Hilbert Curve [wikipedia.org] for storing data? Cool!

Re:Hilbert Curve (0)

Anonymous Coward | more than 4 years ago | (#29763885)

Yeah that crazy life! Always figuring things out.

Re:Hilbert Curve (1)

Sulphur (1548251) | more than 4 years ago | (#29764823)

Hilbert peeked.

Re:Hilbert Curve (4, Funny)

swanzilla (1458281) | more than 4 years ago | (#29764131)

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 (1)

telomerewhythere (1493937) | more than 4 years ago | (#29764325)

And to top it off, it was ... Clever!!!

FTA:

"Cells cleverly separate the most active genes into their own special neighborhood, to make it easier for proteins and other regulators to reach them," says Job Dekker, associate professor of biochemistry and molecular pharmacology at UMass Medical School and a senior author of the Science paper.

Re:Hilbert Curve (3, Insightful)

Artifakt (700173) | more than 4 years ago | (#29764815)

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.

Re:Hilbert Curve (1)

telomerewhythere (1493937) | more than 4 years ago | (#29765365)

\tangent

Actually I wonder if this will sway any minds on the "Is math discovered or invented?" debate.

/tangent

But back on the subject... I have often wondered why life seems to have this innate 'desire' to stay alive (or at least propagate/procreate) Maybe that's the biggest anthropomorphical statement of all???

Obligatory (5, Funny)

davidwr (791652) | more than 4 years ago | (#29763431)

All your base-pair are belong to us.

Re:Obligatory (0, Troll)

mhajicek (1582795) | more than 4 years ago | (#29763513)

Mod parent funny.

Re:Obligatory (0)

Anonymous Coward | more than 4 years ago | (#29763671)

I'm glad you would, because it doesn't seem like anyone else is still amused by AYBABTU.

Re:Obligatory (0, Funny)

Anonymous Coward | more than 4 years ago | (#29763697)

Mod your mom ugly.

Re:Obligatory (3, Insightful)

wexsessa (908890) | more than 4 years ago | (#29763777)

"All your base-pair are belong to us" True in some cases, unfortunately, thanks to the USPTO allowing patents on naturally-occurring structures.

OH YEAH!!!! (3, Funny)

Red Flayer (890720) | more than 4 years ago | (#29763437)

FTA:

In the past, many scientists had thought that DNA was compressed into a different architecture called an "equilibrium globule," a configuration that is problematic because it can become densely knotted and does not easily open up.

Key to deciphering the genome's structure was the development of the new Hi-C technique, which permits genome-wide analysis of the proximity of individual genes.

When questioned about the research, Kool-Aid Man [google.com] could only sob dejectedly as his rival took the glory.

Re:OH YEAH!!!! (1)

hldn (1085833) | more than 4 years ago | (#29765113)

i'm willing to bet ecto cooler was involved.

So.... (2, Interesting)

RabidMoose (746680) | more than 4 years ago | (#29763463)

So, what you're telling me, is that DNA naturally defragments itself, in order to be usable even in an archived state?

Re:So.... (3, Interesting)

interval1066 (668936) | more than 4 years ago | (#29763867)

And it makes use of a primary cache. "That's hot."

Re:So.... (1)

Machupo (59568) | more than 4 years ago | (#29765053)

How long until some Akhibara electro-wizard overclocks your DNA with LN?

Fascinating (4, Insightful)

Taibhsear (1286214) | more than 4 years ago | (#29763575)

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 (4, Insightful)

wizardforce (1005805) | more than 4 years ago | (#29763699)

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.

Re:Fascinating (1)

wexsessa (908890) | more than 4 years ago | (#29763787)

"Future considerations".

Re:Fascinating (0, Flamebait)

Slicebo (221580) | more than 4 years ago | (#29763701)

No.

Re:Fascinating (5, Informative)

Daniel Dvorkin (106857) | more than 4 years ago | (#29763873)

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.

Re:Fascinating (0)

Requiem18th (742389) | more than 4 years ago | (#29763955)

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.

Re:Fascinating (-1, Troll)

Anonymous Coward | more than 4 years ago | (#29764125)

And we should listen to your bullshit uneducated assumptions because? You dumb fucking hick, go back to fucking your goats, fuckface.

Re:Fascinating (2, Interesting)

wizardforce (1005805) | more than 4 years ago | (#29764127)

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).

Re:Fascinating (2, Interesting)

Requiem18th (742389) | more than 4 years ago | (#29764399)

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".

Re:Fascinating (1, Insightful)

Anonymous Coward | more than 4 years ago | (#29765111)

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.

Re:Fascinating (0)

Anonymous Coward | more than 4 years ago | (#29764257)

if it was there for structural purposes it would consist of the same base-pair repeated over and over

Dear sir, you are an idiot and a cretin for making such a bold assertion without supporting it. If the junk DNA served structural purposes and nothing else, then what difference does it make whether it consists of the same base pair, or base pairs from old genes, pray tell?

You appear to be an ignorant, arrogant and stupid biology major with self esteem issues. Please fuck off and die quietly, you sack of rancid human shit.

Re:Fascinating (2, Informative)

mollusc (746594) | more than 4 years ago | (#29764313)

Just because a section of DNA doesn't encode a protein doesn't make it useless. A lot of that stuff is transcribed, and I'm pretty sure cells don't transcribe garbled gibberish just for the hell of it.

Re:Fascinating (2, Insightful)

tftp (111690) | more than 4 years ago | (#29765475)

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 (3, Insightful)

Daniel Dvorkin (106857) | more than 4 years ago | (#29765151)

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.

Re:Fascinating (1, Interesting)

Requiem18th (742389) | more than 4 years ago | (#29765295)

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, vestigial genes. Also while it might be true that a single base pair repeated over and over as I suggested could not be viable, simpler arrangements should be possible and indeed, we have deleted sections of it in flies and bacteria without noticeable effects.

I'm not against or in pro of the term junk DNA, what bugs me is the scare quotes, the haha "junk" DNA is not junk after all take that science! stance of the ID drones.

Re:Fascinating (4, Funny)

d474 (695126) | more than 4 years ago | (#29764031)

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 (5, Funny)

amRadioHed (463061) | more than 4 years ago | (#29764849)

Real gods don't comment their code. It was hard to write, it should be hard to read.

Re:Fascinating (0)

Anonymous Coward | more than 4 years ago | (#29764113)

There is truly "junk" DNA in our genomes. This study http://www.nature.com/nature/journal/v431/n7011/full/nature03022.html showed how removing 2.4 million base pairs from a mouse's genome still maintained the critter's viability.

Re:Fascinating (2, Informative)

rnaiguy (1304181) | more than 4 years ago | (#29764339)

I could remove your eyes, spleen, appendix, and much much more, and you'd still be viable. Doesn't make it junk.

oh, _sure_ (1)

Onymous Coward (97719) | more than 4 years ago | (#29764419)

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.

"Junk" = regulatory RNA (2, Informative)

mollusc (746594) | more than 4 years ago | (#29764287)

Probably not - it's doing something far more important than that.

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 [uq.edu.au] 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. [cam.ac.uk] 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.

Re:"Junk" = regulatory RNA (1)

Machupo (59568) | more than 4 years ago | (#29765101)

good point -- though the DNA is non-coding, it's structural conformation alone can affect the expression of other factors in the coding DNA.

Re:"Junk" = regulatory RNA (1)

mollusc (746594) | more than 4 years ago | (#29765395)

It's got nothing to do with the DNA structure: the DNA is transcribed to RNA, usually very small pieces of RNA, and they regulate proteins and other bits of RNA in complex and still poorly understood ways.

Re:Fascinating (1)

v1 (525388) | more than 4 years ago | (#29764443)

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.

An obvious question arises... (1)

jmerlin (1010641) | more than 4 years ago | (#29763601)

how exactly did the DNA get folded in this manner?

Re:An obvious question arises... (0)

Anonymous Coward | more than 4 years ago | (#29763663)

Magic!

Re:An obvious question arises... (1)

Sulphur (1548251) | more than 4 years ago | (#29764901)

Majic 102

Re:An obvious question arises... (0)

Anonymous Coward | more than 4 years ago | (#29763863)

God! ....I'll see myself out.

Re:An obvious question arises... (2, Informative)

MozeeToby (1163751) | more than 4 years ago | (#29764005)

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... (5, Informative)

reverseengineer (580922) | more than 4 years ago | (#29765037)

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.

Re:An obvious question arises... (0)

Anonymous Coward | more than 4 years ago | (#29764237)

A wizard did it.

Re:An obvious question arises... (1)

telomerewhythere (1493937) | more than 4 years ago | (#29765501)

The same way proteins fold...We don't know...

Re:An obvious question arises... (2, Insightful)

Will.Woodhull (1038600) | more than 4 years ago | (#29765573)

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.

How? (1)

Thelasko (1196535) | more than 4 years ago | (#29763609)

How is DNA folded into the nucleus of a cell without being tangled?

Very carefully.

Great (2, Funny)

thewils (463314) | more than 4 years ago | (#29763611)

Now maybe Apple could apply this structure to my iPod earphones. They're _always_ getting tangled.

Re:Great (3, Informative)

troylanes (883822) | more than 4 years ago | (#29763783)

I used to have this problem, too, until I discovered that little white collar on the wire. When not in use, simply slide it all the way up. This prevents the majority of the knotting. Or, just get a pair that occupy 4 dimensional space -- that way it's impossible for them to get tangled up!

Re:Great (1)

thewils (463314) | more than 4 years ago | (#29763983)

The little white collar on 4Gen Shuffles doesn't go all the way up now, the controller gets in the way.

Re:Great (1)

thewils (463314) | more than 4 years ago | (#29764013)

Hey!!!

Re:Great (1)

rsborg (111459) | more than 4 years ago | (#29764611)

The little white collar on 4Gen Shuffles doesn't go all the way up now, the controller gets in the way.

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.

Re:Great (1)

amRadioHed (463061) | more than 4 years ago | (#29764885)

Or, just get a pair that occupy 4 dimensional space -- that way it's impossible for them to get tangled up!

Ever see a klein bottle? You have no idea the nasty tangles an extra dimension can get you into.

Re:Great (2, Funny)

LoverOfJoy (820058) | more than 4 years ago | (#29764955)

I hate it when my schwartz gets tangled.

worlds smallest (1)

binaryseraph (955557) | more than 4 years ago | (#29763721)

origami. I hope they can fold my DNA into crane... or a box.

Re:worlds smallest (0)

Anonymous Coward | more than 4 years ago | (#29764165)

What a retarded and braindead response. If I had mod points, you would get -1 immediately. Please delete yourself from the gene pool as quickly and cleanly as you can, which, for an idiotic cretin like you, will probably mean a shotgun barrel in the mouth.

Re:worlds smallest (1)

Onymous Coward (97719) | more than 4 years ago | (#29764681)

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.

Globules (1)

Absolut187 (816431) | more than 4 years ago | (#29763743)

My take-away:

DNA looks like a rubik's cube made out of colored spaghetti.

Under the old theory, the rubik's spaghetti-sphere looks like it hasn't been solved yet.
But under the new theory, the puzzle is solved and all the blue shit is next to all the other blue shit, and so on.

http://web.mit.edu/newsoffice/2009/3d-genome.html [mit.edu]

Folding @ Home (0)

Anonymous Coward | more than 4 years ago | (#29763819)

So, was this project a huge success?

Cake for everyone. It's not a lie.

Boo, article. (0)

Anonymous Coward | more than 4 years ago | (#29763875)

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.

good job (1)

mapkinase (958129) | more than 4 years ago | (#29764059)

Nice to see 2 familiar names in one article (Grosberg/Mirny)...

What about beads on a string? (3, Interesting)

angrytuna (599871) | more than 4 years ago | (#29764385)

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? (5, Informative)

Anonymous Coward | more than 4 years ago | (#29764619)

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.

Re:What about beads on a string? (1, Informative)

Anonymous Coward | more than 4 years ago | (#29765137)

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.

Re:What about beads on a string? (3, Informative)

Anonymous Coward | more than 4 years ago | (#29765167)

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.

This study shows that DNA is packed into the nucleus in an ordered fashion, by direct observation of all the spatially close bits. These end up not being random at all. Instead they are consistent with a fractal globule. I'd never heard of these before, but they have some interesting properties with regard to tangling. Which is probably the best thing about this for me, polymers of this length should tend to get horribly tangled, which would be bad, given that the cell has to split them up every time it divides.

Overall, very neat, really hard work.

-sk

Re:What about beads on a string? (0)

Anonymous Coward | more than 4 years ago | (#29765327)

This is about what happens to the DNA when it's NOT in the Chromatin metaphase.

Better picture (0)

Anonymous Coward | more than 4 years ago | (#29764435)

This article [scienceblogs.com] has a picture that shows the location of the fractal globule.

Anyone else wish they could read the publication? (4, Insightful)

virtualXTC (609488) | more than 4 years ago | (#29764543)

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.

Re:Anyone else wish they could read the publicatio (1)

virtualXTC (609488) | more than 4 years ago | (#29764755)

I guess I'll have to wait the 12 months as per the NIH policy.

Wow... (1)

Dausha (546002) | more than 4 years ago | (#29764569)

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... (4, Informative)

Dr. Manhattan (29720) | more than 4 years ago | (#29764993)

Quite intelligent. Not at all random, if I may say so myself.

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.

Re:Wow... (0)

Anonymous Coward | more than 4 years ago | (#29765235)

"take a complex number... square it... add the original number"... I CAN'T UNDERSTAND a fucking thing of what you are saying... how am I supposed to DO it?

Re:Wow... (1)

Machupo (59568) | more than 4 years ago | (#29765089)

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 (1)

Peaker (72084) | more than 4 years ago | (#29765201)

You are ignorant about evolution. Anyone who says evolution is "random" doesn't know the first thing about evolution.

Re:Unfortunately (0, Flamebait)

Dausha (546002) | more than 4 years ago | (#29765293)

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.

How humans would have designed it? (0)

Anonymous Coward | more than 4 years ago | (#29764575)

If humans had a task to engineer a solution for this task, how would we do it?

I call dibs on the patent (0)

Anonymous Coward | more than 4 years ago | (#29764725)

I patent this new invention! You all owe me money or you may not reproduce!

I am very disappointed... (3, Funny)

Jah-Wren Ryel (80510) | more than 4 years ago | (#29765441)

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.

This is not news. (1)

clayski (214528) | more than 4 years ago | (#29765527)

This concept has been the subject of several review articles in the scientific journal Nature - as early as 2007to my knowledge.

Load More Comments
Slashdot Login

Need an Account?

Forgot your password?

Submission Text Formatting Tips

We support a small subset of HTML, namely these tags:

  • b
  • i
  • p
  • br
  • a
  • ol
  • ul
  • li
  • dl
  • dt
  • dd
  • em
  • strong
  • tt
  • blockquote
  • div
  • quote
  • ecode

"ecode" can be used for code snippets, for example:

<ecode>    while(1) { do_something(); } </ecode>