Scientists say they’ve found a code beyond genetics in DNA

July 25, 2006 4:21 AM

Scientists say they’ve found a code beyond genetics in DNA. The study by Segal et al. [PDF] establishes a model for predicting some (but not all) nucleosome placement. This is critical for understanding the regulation of gene expression.
posted by rxrfrx (31 comments total)

Interestingly, the model might have been even better if it weren't for the fact that researchers can't agree on where some of the nucleosomes actually are.
posted by rxrfrx at 4:24 AM on July 25, 2006

The discovery, if confirmed, could open new insights into the higher order control of the genes, like the critical but still mysterious process by which each type of human cell is allowed to activate the genes it needs but cannot access the genes used by other types of cell.

Does that mean they could essentially turn any cell into a stem cell? This all sounds vaguely important, but I'm not clear on how exactly.
posted by scottreynen at 4:56 AM on July 25, 2006

Any cell could be potentially turned into a stem cell- but first we have to know how stem cells are different from differentiated ones, and how we would change the state of a differentiated cell to regain those necessary characteristics of a stem cell.

This is just a piece of that puzzle, but it's a big step toward understanding how animal cells might decide which genes will be turned on and off, and when.
posted by rxrfrx at 5:15 AM on July 25, 2006

But how does it practically help us to know how animal cells might decide which genes will be turned on and off? This science...it vibrates?
posted by scottreynen at 5:43 AM on July 25, 2006

Everything vibrates, as long as there's a temperature above 0 Kelvin.

But, I think what the article and rxrfrx are saying is that by learning where the nucleosomes are placed in relation to genes that are on (or off) then we can apply this to other cells types and predict whether or not their genes will be on (or off) depending solely on where the nucleosomes are placed.
posted by LunaticFringe at 5:48 AM on July 25, 2006 [2 favorites]

posted by Plutor at 5:51 AM on July 25, 2006

Considering that the science of genetics predates the discovery of DNA and the article is about the role of nucleosomes shouldn't the headline state: Scientists Say They’ve Found a Code Beyond Codons in Genetics?
posted by Human Flesh at 5:58 AM on July 25, 2006

In a probabilistic sense, a higher level of information in what you're looking at makes it easier to correctly guess what it represents. That is, its probability distribution favors certain outcomes — for example, this DNA should associate with that nucleosome.

Given how histones and histone structure modifications are highly conserved over generations and species, it's not surprising they contain information that can be turned into probabilistic patterns we can exploit.

Predictibility (probability distributions) in the genetic outcome is, after all, how we deciphered the genetic code in the first place, which was done even before the structure of DNA was understood.
posted by Blazecock Pileon at 6:15 AM on July 25, 2006

This is important information Scottreynen, but the "this could lead to" speculation at the end sounds like the "this could lead to" speculation at the end of every science news article for the layman. I can'd find the exact quote but someone involved in Bose-Einstein Condensate project said, when asked what it was good for, said something like, "When they invented the laser they had all these ideas about using it to slice steel like butter and laser weapons. Nobody said a word about data storage or eye surgery. So I'm going to say, I don't know."

Every scientist ought to take a class on explaining things to non-scientists and that ought to be the first lesson. In the short term it's just cool to know this stuff. In the long term, well, do a pattent search on any number of biochemical terms.

We knew there was something there, and now we seem to know how it works. The next steps involve figuring out what all it is attached to. After that we can start thinking about how to tell a cancer cell, "Hey, do me a favor and bury that gene right there."
posted by Kid Charlemagne at 6:29 AM on July 25, 2006 [2 favorites]

Human Flesh, good point about the distinction btwn codons and genetics. This is a higher-order genetic code, but it is still in the realm of genetics.

This discovery is huge, if it is the real deal. What these scientists MAY have discovered is a code for "super genes" that dictate higher-order structure of chromosomes. Perhaps there is something in this code that dictates expression of gene products as well. This may help us understand the reason for vast sequences of apparently useless "filler" in the chromosomes - most of the DNA does not code a readily apparent "product", but it may be doing other important things, like determining 3D structure.

Forget about stem cells, or any other therapeutic application for the moment. This kind of pure science is the key to gaining deeper insight into the mysteries of life [cue eerie music]; don't let the fact that it won't immediately cure fatness or anything diminish your appreciation of its importance.
posted by Mister_A at 6:58 AM on July 25, 2006

Metafilter: a temperature above 0 Kelvin
posted by nofundy at 7:19 AM on July 25, 2006

Mmm. Blood Music.
posted by loquacious at 7:24 AM on July 25, 2006

I got a chuckle out of the implication, intentional or not, in the last sentence: Biologists have long speculated that the redundancy may have been designed so as to coexist with some other kind of code, and this, Dr. Segal said, could be the nucleosome code.
posted by beagle at 7:27 AM on July 25, 2006

Dr. Norris is way badder than Dr. Segal.
posted by Smedleyman at 7:47 AM on July 25, 2006

This may help us understand the reason for vast sequences of apparently useless "filler" in the chromosomes

True, this is a possibility. But much of so-called junk DNA is highly variable and, therefore, probably a bad fit for a regulatory code which appears to be highly conserved across taxa.
posted by docgonzo at 8:05 AM on July 25, 2006

Totally off-topic, but "Everything vibrates, as long as there's a temperature above 0 Kelvin" is the ultimate rejoinder to end all "This X... it vibrates?" jokes. It should be sidebarred. LunaticFringe, you are truly the king of the Internets.
posted by goodnewsfortheinsane at 8:07 AM on July 25, 2006

we deciphered the genetic code in the first place, which was done even before the structure of DNA was understood.

Huh? Watson and Crick published the double helix in 1953; even your link says the genetic code was deciphered in the late '50s to 1961.

It wasn't clear to me that what they've found has direct impact on gene expression, but maybe I didn't read closely enough. Still a big step forward.
posted by Joe Invisible at 8:09 AM on July 25, 2006

nucleosome nucleawesome

I'm so glad everything vibrates.
posted by CynicalKnight at 8:13 AM on July 25, 2006

But can Monsanto patent it? That's the question.
posted by ZenMasterThis at 8:15 AM on July 25, 2006

I figure the "genetics" referred to in the headline denotes heritable phenotypes (as opposed to regulatory sequences). Of course, we've known about that for a long time.
posted by rxrfrx at 8:17 AM on July 25, 2006

But can Monsanto patent it? That's the question.

Now that it's been published, no. But they could've.
posted by rxrfrx at 8:17 AM on July 25, 2006

"More human than human is our motto..."
Eldon Tyrell, Tyrell Corporation
posted by QuestionableSwami at 8:45 AM on July 25, 2006

Pattenting basic research is wasted time and money. It doesn't stop anyone from playing with it in the lab and nothing commercializable is going to come of it until after the patent runs out.

Now, if somebody took this discovery and did something that saved lives with it, I think they deserve the 17 year window that a patent gives them. Mickey Mouse hasn't saved anyone's life and he gets more than 50 years of protection.
posted by Kid Charlemagne at 9:13 AM on July 25, 2006

Every scientist ought to take a class on explaining things to non-scientists and that ought to be the first lesson.
posted by Kid Charlemagne

That is a good idea, but how do you get people past the idea that "science is hard" and scientists should be correspondingly smart and inaccessible? Reporters no longer treat scientists as unassailable sources, but the problem is still there, and in my experience it's a real barrier.
posted by zennie at 9:57 AM on July 25, 2006

What assurances do we have that Dan Brown won't use this code as a badly researched gimmick for a novel?
posted by Iridic at 10:12 AM on July 25, 2006

Pattenting basic research is wasted time and money. It doesn't stop anyone from playing with it in the lab and nothing commercializable is going to come of it until after the patent runs out.

Hm, what about PCR? Taq polymerase? Restriction enzymes? Those were commercialized, despite (because of?) patent protection.
posted by Joe Invisible at 10:13 AM on July 25, 2006

The basic concept of a restriction enzyme wasn't patented. The basic concept of a purified polymerase wasn't patented.

And well, they tried to lock people down on PCR but of course they couldn't stop people in the lab, so the patent protection really only extended to diagnostic uses.
posted by rxrfrx at 10:16 AM on July 25, 2006

I read in a textbook that it was controlled by the frequency of certain nucleotides. That seems to be what they're saying here, but they don't actually say what the "code" is that they've found. If that's it, it's not new at all, maybe just more confirmation.

Kind of a stupid article, IMO.
posted by delmoi at 11:03 AM on July 25, 2006

delmoi, did you RTFA? How could you have missed grafs two and three?

"Thus, nucleosomes have substantial DNA sequence preferences. A key question is whether genomes use these sequence preferences to control the distribution of nucleosomes in vivo in a way that strongly impacts on the ability of DNA binding proteins to access particular binding sites. By controlling binding site accessibility in this way, genomes could, for example, target the binding of transcription factors towards appropriate sites and away from irrelevant, non-functional sites.
Our view is that the sequence preferences of nucleosomes might not be meaningful."

Emphasis mine.
posted by docgonzo at 11:55 AM on July 25, 2006

There is a lot of not yet known information in the non-gene parts of DNA. At a conference in January I first heard another story of new patterns in DNA. It's all quite exciting, because it means there is still more to learn. (And a relief to know that it's not just "junk DNA" - that would have been such a waste)
posted by easternblot at 5:40 PM on July 25, 2006

rxrfrx, Sounds exciting. Thanks for this post. Wish I understood it better and look forward to learning about this more.
posted by nickyskye at 9:44 AM on July 26, 2006