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Scientists discover double meaning in genetic code

 
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kamalktkOffline
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PostPosted: 13-12-2013 13:17    Post subject: Scientists discover double meaning in genetic code Reply with quote

Not messages from aliens... yet.

http://www.washington.edu/news/2013/12/12/scientists-discover-double-meaning-in-genetic-code/

Scientists have discovered a second code hiding within DNA. This second code contains information that changes how scientists read the instructions contained in DNA and interpret mutations to make sense of health and disease.
J Stam

Genome scientist Dr. John Stamatoyannopolous led a team that discovered a second code hidden in DNA.

A research team led by Dr. John Stamatoyannopoulos, University of Washington associate professor of genome sciences and of medicine, made the discovery. The findings are reported in the Dec. 13 issue of Science. The work is part of the Encyclopedia of DNA Elements Project, also known as ENCODE. The National Human Genome Research Institute funded the multi-year, international effort. ENCODE aims to discover where and how the directions for biological functions are stored in the human genome.

Since the genetic code was deciphered in the 1960s, scientists have assumed that it was used exclusively to write information about proteins. UW scientists were stunned to discover that genomes use the genetic code to write two separate languages. One describes how proteins are made, and the other instructs the cell on how genes are controlled. One language is written on top of the other, which is why the second language remained hidden for so long.

“For over 40 years we have assumed that DNA changes affecting the genetic code solely impact how proteins are made,” said Stamatoyannopoulos. “Now we know that this basic assumption about reading the human genome missed half of the picture. These new findings highlight that DNA is an incredibly powerful information storage device, which nature has fully exploited in unexpected ways.”

The genetic code uses a 64-letter alphabet called codons. The UW team discovered that some codons, which they called duons, can have two meanings, one related to protein sequence, and one related to gene control. These two meanings seem to have evolved in concert with each other. The gene control instructions appear to help stabilize certain beneficial features of proteins and how they are made.

The discovery of duons has major implications for how scientists and physicians interpret a patient’s genome and will open new doors to the diagnosis and treatment of disease.

“The fact that the genetic code can simultaneously write two kinds of information means that many DNA changes that appear to alter protein sequences may actually cause disease by disrupting gene control programs or even both mechanisms simultaneously,” said Stamatoyannopoulos.

Grants from the National Institutes of Health U54HG004592, U54HG007010, and UO1E51156 and National Institute of Diabetes and Digestive and Kidney Diseases FDK095678A funded the research.

In addition to Stamatoyannopoulos, the research team included Andrew B. Stergachis, Eric Haugen, Anthony Shafer, Wenqing Fu, Benjamin Vernot, Alex Reynolds, and Joshua M. Akey, all from the UW Department of Genome Sciences, Anthony Raubitschek of the UW Department of Immunology and Benaroya Research Institute, Steven Ziegler of Benaroya Research Institute, and Emily M. LeProust, formerly of Agilent Technologists and now with Twist Bioscience.
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MythopoeikaOffline
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PostPosted: 13-12-2013 20:29    Post subject: Reply with quote

It's probably a maker's mark.
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Pietro_Mercurios
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PostPosted: 13-12-2013 21:17    Post subject: Reply with quote

Wonder what other surprises are tucked away in there?
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JamesWhiteheadOffline
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PostPosted: 13-12-2013 22:59    Post subject: Reply with quote

I regret to inform you that our company can no longer insure you, since your genetic code has revealed a susceptibility to Mrs Slocumbe's Pussy! Shocked

edit: Slocumbe! not as orignally spelled. Embarassed
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jimv1Offline
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PostPosted: 14-12-2013 12:04    Post subject: Reply with quote

Hmmmmmmm.
So that means scientists opened the genie bottle and have been developing GM crops and godknowswhatelse with only a fraction of the knowledge they thought they had.

Not exactly reassuring.
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MercuryCrestOffline
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PostPosted: 14-12-2013 22:48    Post subject: Reply with quote

This article from Forbes seems a little more grounded. Or bitchy. Whichever....

From: http://www.forbes.com/sites/emilywillingham/2013/12/13/dont-be-duped-by-duon-dna-hype/

Quote:
Don't Be Duped By 'Duon' DNA Hype

With today’s headlines hyping “Second Code Uncovered Inside the DNA,” you might think that scientists are running around in circles in their labs, tearing out their hair, and screaming, “Crick, you loser!” But the real reaction of scientists to these headlines is more along the lines of this Twitter conversation among several scientific experts and science writers. They have good reason to be snarky.

The hype began with the way hype often begins: an institutional news release offering us the holy grail/huge breakthrough/game-changing finding of the day. This kind of exaggeration is the big reason any science consumer should look well beyond the news release in considering new findings. A news release is a marketing tool. You’re reading an advertisement when you read a news release. In this case, the advertisement/news release not only goes off the rails with the hype, it’s also scientifically garbled and open to all kinds of misinterpretation, as the comments at the link to the release make clear.

Here’s some of the hype with a soupçon of garble.

Since the genetic code was deciphered in the 1960s, scientists have assumed that it was used exclusively to write information about proteins. UW scientists were stunned to discover that genomes use the genetic code to write two separate languages.

Scientists have not assumed that the genetic code “was used exclusively to write information about proteins,” or even ever assumed that it “writes information about proteins,” whatever that means. A quick primer: Proteins are molecules that do the work of an organism, and that includes the work of copying DNA for protein production and cell division. Even nonmajors biology textbooks cover the fact that the DNA sequence both contains code for proteins and serves a regulatory purpose, making it possible to copy that code into a form the cell can read, recipe-like, to build the proper protein. We even have names for these regulatory DNA sequences: promoters, enhancers, termination sequences. (edited) I’d be stunned if UW scientists were genuinely “stunned” to discover this dual use of DNA sequences to “write” “two separate languages” because what they really describe is the use of a single language, the language of nucleotides, for two known purposes. They themselves noted that “the potential for some coding exons to accommodate transcriptional enhancers or splicing signals has long been recognized.”

The release quotes study author John Stamatoyannopoulos as saying that

For over 40 years we have assumed that DNA changes affecting the genetic code solely impact how proteins are made,” said Stamatoyannopoulos. “Now we know that this basic assumption about reading the human genome missed half of the picture. These new findings highlight that DNA is an incredibly powerful information storage device, which nature has fully exploited in unexpected ways.”

I can only hope that Stamatoyannopoulos didn’t really say that. The authors report that changes in a single DNA sequence can influence both the protein it encodes and the place where other proteins bind to initiate copying. So evolutionarily, a single change could influence two endpoints–copying the sequence and what gets made using the same sequence. That’s cool, but not actually new. How it goes beyond “solely impact(ing) how proteins are made” goes beyond me, and it certainly doesn’t miss half the picture. Indeed, based on the study itself (paywalled), it could possibly have missed up to a fifth of the picture.

The release also contains gems such as “The genetic code uses a 64-letter alphabet called codons.” This sentence makes me sad. Codons consist of three nucleotides–which we designate with the letters A, C, G, and T/U–and there are 64 of these triplets, 61 of which serve as molecular code words for 20 amino acids (here is a DNA nucleotide codon table, too; these are the codons the authors address). Some amino acids get more than one word to designate them. The cell “reads” these code words and uses the amino acids they designate to build proteins. There.

(Update) The other problem is the ubiquitous use of the phrase “second code” in so many of the headlines related to this story when the authors themselves state: “ Although nearly all codon biases parallel TF recognition preferences genome-wide…” with the arginine codon as an exception. That’s not a “second code,” even though the news release describes it that way. It’s a different (but already recognized) use of an existing code, now identified as occurring at a greater than previously recognized frequency in areas that use the same code for proteins.

So what was the real import of the study that warranted its publication in Science, a “glamor” science publication? The authors (whose paper I enjoyed) seem to have found that the genome contains more of these dual-use triplet DNA sequences than previously thought, which might make them more relevant when examining some aspects of evolution (see “Single change could influence two endpoints”). And, it seems, the authors wanted the opportunity to, um, codify their own term for these dual-use sequences: duons. I wonder if they realized that the name had already been taken?
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UrvogelOffline
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PostPosted: 15-12-2013 20:14    Post subject: Reply with quote

jimv1 wrote:
Hmmmmmmm.
So that means scientists opened the genie bottle and have been developing GM crops and godknowswhatelse with only a fraction of the knowledge they thought they had.

Not exactly reassuring.


In all fairness the first cavemen who saw their friend mate two woolly sheep to make even woollier sheep were probably thinking the same thing.
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rynner2Offline
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PostPosted: 15-12-2013 21:26    Post subject: Reply with quote

Urvogel wrote:
jimv1 wrote:
Hmmmmmmm.
So that means scientists opened the genie bottle and have been developing GM crops and godknowswhatelse with only a fraction of the knowledge they thought they had.
Not exactly reassuring.

In all fairness the first cavemen who saw their friend mate two woolly sheep to make even woollier sheep were probably thinking the same thing.

And even Darwin and Mendel knew nothing about DNA, but they did know some things about breeding.

So the discovery in 1953 of the double-helix, with all its implications
http://www.nobelprize.org/educational/medicine/dna_double_helix/readmore.html
was a huge leap forward.

No doubt these new discoveries will one day be seen the same way, but it doesn't mean that everything we've learnt so far has to be thrown out of the window. It's all still true, as far as it goes, but now there is an extra level of complexity to explore. Our horizons just got wider, just as they did in Darwin's day, and then (not exactly in, but after) Mendel's day (because his work was ignored for many years).
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jimv1Offline
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PostPosted: 17-12-2013 00:19    Post subject: Reply with quote

A sheep and a sheep are still sheep.

Using jellyfish DNA to make rabbits that glow in the dark is quite different.

God knows what weird strains have been tried and tested. Having said that I am extremely disappointed with the Spidergoats.
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Anome_Offline
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PostPosted: 17-12-2013 09:17    Post subject: Reply with quote

Yes, the great promise of cheap spider silk materials doesn't seem to have been fulfilled.

I haven't had a chance to properly review the papers yet, but my understanding is that this is one of the missing pieces of genetics. We know that particular sequences in DNA do particular things, but we're still working through what turns different genes on and off, and I think this is part of that.
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rynner2Offline
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PostPosted: 17-12-2013 09:26    Post subject: Reply with quote

jimv1 wrote:
A sheep and a sheep are still sheep.

What sheep breeders (and breeders of all other farmyard and domestic creatures) were actually doing, even though they didn't realise it before Mendel's ideas about genes became widely known, was changing the frequency of genes in their creations.

Nature had provided the Ur-sheep with a set of genes that worked pretty well it its original environment, but when humans started farming them the humans wanted the sheep to produce more milk, or meat, or wool etc, and they did this by artificial selection of which animals were allowed to breed. But this meant some genes got preferential treatment, and gradually the gene-set changed.

At the molecular level, all genes, whether animal or vegetable, are similar, and we now have the skills to mix and match them as we choose. I don't want to get into a big debate about GM, but merely to point out that it's only a modern way of doing what animal and vegetable breeders have been doing for thousands of years.
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