Are genes our destiny? 'Hidden' code in DNA evolves more rapidly than genetic code, scientists discover

Sep 16, 2011
A photo of an Arabidposis plant. Credit: Joe Belcovson, Salk Institute for Biological Studies

A "hidden" code linked to the DNA of plants allows them to develop and pass down new biological traits far more rapidly than previously thought, according to the findings of a groundbreaking study by researchers at the Salk Institute for Biological Studies.

The study, published today in the journal Science, provides the first evidence that an organism's "epigenetic" code - an extra layer of biochemical instructions in DNA - can evolve more quickly than the genetic code and can strongly influence biological traits.

While the study was limited to a single called Arabidopsis thaliana, the equivalent of the laboratory rat of the plant world, the findings hint that the traits of other organisms, including humans, might also be dramatically influenced by that scientists are just beginning to understand.

"Our study shows that it's not all in the genes," said Joseph Ecker, a professor in Salk's Plant Laboratory, who led the research team. "We found that these plants have an epigenetic code that's more flexible and influential than we imagined. There is clearly a component of heritability that we don't fully understand. It's possible that we humans have a similarly active epigenetic mechanism that controls our biological characteristics and gets passed down to our children. "

With the advent of techniques for rapidly mapping the DNA of organisms, scientists have found that the genes stored in the four-letter don't always determine how an organism develops and responds to its environment. The more biologists map the genomes of various organisms (their entire genetic code), the more they are discovering discrepancies between what the genetic code dictates and how organisms actually look and function.

In fact, many of the major discoveries that led to these conclusions were based upon studies in plants. There are traits such as flower shape and fruit in some plants that are under the control of this epigenetic code. Such traits, which defy the predictions of classical Mendelian genetics, are also found in mammals. In some strains of mice, for instance, a tendency for obesity can pass from generation to generation, but no difference between the genetic code of fat mice and thin mice explains this weight difference.

Scientists have even found that identical human twins exhibit different biological traits, despite their matching DNA sequences. They have theorized that such unexplained disparities could be the work of epigenetic variation.

"Since none of these patterns of variation and inheritance match what the genetic sequence says should happen, there is a clearly a component of the 'genetic' that is missing," Ecker said.

Ecker and other scientists have traced these mysterious patterns to chemical markers that serve as a layer of genetic control on top of the DNA sequence. Just as genetic mutations can arise spontaneously and be inherited by subsequent generations, epigenetic mutations can emerge in individuals and spread into the broader population.

Although scientists have identified a number of epigenetic traits, very little was known about how often they arose spontaneously, how quickly they could spread through a population and how significant an influence they could have on biological development and function.

"Perception of the extent of epigenetic variation in plants from generation to generation varies widely within our scientific community," said Robert Schmitz, a post-doctoral research in Eckers' laboratory and the lead author on the paper. "We actually did the experiment, and found that overall there is very little change between each generation, but spontaneous epimutations do exist in populations and arise at a rate much higher than the DNA mutation rate, and at times they had a powerful influence over how certain genes were expressed."

In their study, the Salk researchers and collaborators at Scripps Research Institute mapped the epigenome of a population of Arabidopsis plants then observed how this biochemical landscape had changed after 30 generations. This mapping consisted of recording the state of all locations on the DNA molecule that could undergo a chemical modification known as methylation, a key epigenetic change that can alter how certain underlying genes are expressed. They then watched how methylation states of these sites evolved over the generations.

The plants were all clones of a single ancestor, so their DNA sequences were essentially identical across the generations. Thus any changes in how the plants expressed certain genetic traits were likely to be a result of spontaneous changes in their epigenetic code - variations in the methylation of the DNA sites- not the result of variations in the underlying DNA sequences.

"You couldn't do this kind of study in humans, because our DNA gets shuffled each generation," Ecker said. "Unlike people, some plants are easily cloned, so we can see the epigenetic signature without all the genetic noise."

The researchers discovered that as many as a few thousand methylation sites on the plants' DNA were altered each generation. Although this represents a small proportion of the potentially six million methylation sites estimated to exist on Arabidopsis DNA, it dwarfs the rate of spontaneous change seen at the DNA sequence level by about five orders of magnitude.

This suggests that the epigenetic code of plants - and other organisms, by extension - is far more fluid than their .

Even more surprising was the extent to which some of these changes turned genes on or off. A number of plant genes that underwent heritable changes in methylation also experienced substantial alterations in their expression - the process by which genes control cellular function through protein production.

This meant that not only was the epigenome of the plants morphing rapidly despite the absence of any strong environmental pressure, but that these changes could have a powerful influence on the plants' form and function.

Ecker said the results of the study provide some of the first evidence that the epigenetic code can be rewritten quickly and to dramatic effect. "This means that genes are not destiny," he said. "If we are anything like these plants, our epigenome may also undergo relatively rapid spontaneous change that could have a powerful influence on our biological traits."

Now that they have shown the extent to which spontaneous epigenetic mutations occur, the Salk researchers plan to unravel the biochemical mechanisms that allow these changes to arise and get passed from one generation to the next.

They also hope to explore how different environmental conditions, such as differences in temperature, might drive epigenetic change in the plants, or, conversely, whether epigenetic traits provide the with more flexibility in coping with environmental change.

"We think these epigenetic events might silence genes when they aren't needed, then turned them back on when external conditions warrant," Ecker said. "We won't know how important these epimutations are until we measure the effect on plant traits, and we're just now to the point where we can do these experiments. It's very exciting."

Explore further: Tricking plants to see the light may control the most important twitch on Earth

Related Stories

USC researchers explore genetic causes for male infertility

Dec 12, 2007

Researchers at the University of Southern California (USC) suggest epigenetics, or the way DNA is processed and expressed, may be the underlying cause for male infertility. The study will be published in the Dec. 12 issue ...

Plants display 'molecular amnesia'

Dec 02, 2008

(PhysOrg.com) -- Plant researchers from McGill University and the University of California, Berkeley, have announced a major breakthrough in a developmental process called epigenetics. They have demonstrated for the first ...

Epigenetic signals differ across alleles

Feb 12, 2010

Researchers from the Institute of Psychiatry (IoP), King's College London, have identified numerous novel regions of the genome where the chemical modifications involved in controlling gene expression are influenced by either ...

Scientists clarify a mechanism of epigenetic inheritance

Apr 22, 2008

Although letters representing the three billion pairs of molecules that form the “rungs” of the helical DNA “ladder” are routinely called the human “genetic code,” the DNA they comprise transmits traits across ...

Common orchid gives scientists hope in face of climate change

Aug 10, 2010

A study led by scientists from the Royal Botanic Gardens, Kew's Jodrell Laboratory, which focuses on epigenetics in European common marsh orchids, has revealed that some plants may be able to adapt more quickly to environmental ...

Recommended for you

Getting a jump on plant-fungal interactions

Jul 29, 2014

Fungal plant pathogens may need more flexible genomes in order to fully benefit from associating with their hosts. Transposable elements are commonly found with genes involved in symbioses.

The microbes make the sake brewery

Jul 24, 2014

A sake brewery has its own microbial terroir, meaning the microbial populations found on surfaces in the facility resemble those found in the product, creating the final flavor according to research published ahead of print ...

User comments : 26

Adjust slider to filter visible comments by rank

Display comments: newest first

hush1
1.6 / 5 (11) Sep 16, 2011
1.)"They have theorized that such unexplained disparities could be ..."
2.)"...match what the genetic sequence says should happen,..."
3.)"...how quickly they could spread ..."
4.)"...how significant an influence they could have on..."
5.)"...were likely to be..."
6.)"...but that these changes could have..."
7.)"If we are anything like ..."
8.)"...change that could have ..."
9.)"...might silence genes..."
10.)"...might also be dramatically influenced..."

A flawless article and research except for one fact:
Any words after 'if', 'should', 'could', 'would', 'might', 'maybe' and 'but' are non factual.

Even all commentators/writers will benefit from this realization - not just the research papers published.

And the best part of this English linguistic language marker is there are no exceptions to this.

Not all languages have this downfall. Some make honest use of non factual statements.
wealthychef
5 / 5 (9) Sep 16, 2011
Interesting point, but part of the purpose of the article is to provide context for the research being done, and this of necessity involves speculation since science is about forming theories and then experimenting to see if they can be falsified. There is nothing wrong with speculation; it's clearly labeled as you say. What's erroneous is to read these as if they are statements of fact.
LeChatlier
3.2 / 5 (10) Sep 16, 2011

A flawless article and research except for one fact:
Any words after 'if', 'should', 'could', 'would', 'might', 'maybe' and 'but' are non factual.


Ah, you've found the beauty of science: there are no facts. If more writers took note of this nuance, maybe the sensationalist politicization of science would slow down a little.
hush1
1 / 5 (4) Sep 16, 2011
I adhere to the sentiment expressed by wealthychef and LeChatlier. I ask for crucifixion from readers finding those words in my commentary. Yes, crucifying is a metaphor for correction. I refuse to crucify anyone. Both commentaries show habit, not lack of insight.
Ober
4 / 5 (2) Sep 16, 2011
Well this comes as no surprise to me at all.
After all if chimps share apx 98% the same genetic code as humans, surely 2% doesn't encode directly for the difference.
Also embryos all seem to start the same way, then differentiate.
I'm purely guessing here, but it wouldn't surprise me if MANY creatures are pretty much the same geneticly, and the difference is HOW the genes are expressed.
Just look at how a caterpillar transforms into a butterfly!! It's like two seperate creatures, but we know it's the same one with a different morphology, and thus different gene expression.
I wonder if a butterfly had any sort or memory, whether it could remember anything from the caterpillar stage???? Or is it simpy melt into a chemical soup, rearrange and start again.
So I suspect many creatures are the same, just with different "epigenetic" code.
210
1 / 5 (3) Sep 16, 2011
""Since none of these patterns of variation and inheritance match what the genetic sequence says should happen, there is a clearly a component of the 'genetic' heritability that is missing."
Indeed: Something is either "missing" or relevant but yet unknown. It has occurred to me and to others that demanding that genetics or just 'mutation' account for all the variability/adaptability in the living is just not founded. There IS more because what we have cannot do it all! We know there is change, but insufficient, not absent, insufficient mutation to account for all change. D 'adaptive trigger' has been my point all along & current science is closing N on it, more precisely, this article aims at that piece of nature that says '..time to change/adapt..' we cannot just pooh pooh the work because it did not reach a given point or say what we wanted 2 hear. We cannot discard the journey, D growing body of knowledge & ever get 2 D better land of understanding.
word-to-ya-muthas
210
1.5 / 5 (6) Sep 16, 2011

A flawless article and research except for one fact:
Any words after 'if', 'should', 'could', 'would', 'might', 'maybe' and 'but' are non factual.

Ah, you've found the beauty of science: there are no facts. If more writers took note of this nuance, maybe the sensationalist politicization of science would slow down a little.

Absolute celerity IS a fact.
The Law of Gravity is a fact.
Stoichiometry is a body of fact; The mathematic integral is a fact; Hydrogen fusion is a fact, splitting the atom is made possible by a world...a universe, of facts...etc, etc, etc... The fact that people have made mistakes SEEKING facts IS a fact & not a fact that should excuse error or denounce the pursuit of FACT. We are MORTAL we progress by FAULT: When you were 14, you climbed on your parents house with a cape on, jumped off & broke your arm.Facts dont stop being just because we don't like them!
Thereore, the error of your statement and your belief IS A FACT!
word-to-ya-muthas
kochevnik
3.3 / 5 (10) Sep 16, 2011
The Law of Gravity is a fact.
Actually it's a theory. Gravity is an effect of more fundamental maths/geometry.
The mathematic integral is a fact.
Actually, it's a lemma. The theory of limits implicitly skirts around Zeno's paradox, which has never been unanimously resolved. While we integrate all the time, we should appreciate that we are employing a mental model of reality, which is at best an abstraction. Or, in the case of integration, it's a generalization.
hush1
1 / 5 (2) Sep 17, 2011
Speculation is powerful. Speculation belongs to imagination.
If we don't speculate about facts, then we can remove at least two words from our vocabulary: obsolete and supersede.

Wealthychef and LeChatlier statements are consistent with each other. The ratings must reflect other factors other than consistency.

Facts are like DNA and cosmology. Changing over time. Sometimes the rate of change is exponential.
Deesky
5 / 5 (1) Sep 17, 2011
""Since none of these patterns of variation and inheritance match what the genetic sequence says should happen, there is a clearly a component of the 'genetic' heritability that is missing."
Indeed: Something is either "missing" or relevant but yet unknown.

This article is all over the place, with claims of mysterious effects on the one hand, followed by the explanation of epigenetics. It's very poor form to try to manufacture some kind of mystery to, supposedly keep people interested, when the effect has been known about for some time.

Epigenetics, in its modern meaning, has been known since the 1990s, while the etymology of the term (with slightly different meaning) can be traced to the 50s and 60s. For example, epigenetics plays a role in fur coloration/markings in cats and other mammals, so even if you were to clone your dead pet, it may end up looking totally different (markings wise) than the original.
Parsec
5 / 5 (3) Sep 17, 2011
Ober - chimps and humans share 98% of the genes that code for proteins. The amount we share in transcription regions, epigenic coding, non-coding but important portions of the genome, is a lot smaller, maybe 90%.
210
1.7 / 5 (6) Sep 17, 2011
The Law of Gravity is a fact.
Actually it's a theory. Gravity is an effect of more fundamental maths/geometry.
The mathematic integral is a fact.
Actually, it's a lemma. an abstraction. Or, in the case of integration, it's a generalization.

...which...does NOT, NOT make it any less A FACT...you...and your argument...stilll have the scar tissue to prove it..!
word...
Myno
5 / 5 (1) Sep 17, 2011
If true, this might help to explain how some hermaphrodite populations have survived so long without normal sexual genetic mixing.
frajo
1 / 5 (1) Sep 17, 2011
the genes stored in the four-letter DNA code
Not really. The Wikipedia entry "Genetic code" writes:
With some exceptions, a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid.
Additionally, it contains the RNA and DNA codon tables.
Ethelred
2.3 / 5 (3) Sep 17, 2011
Actually it only codes for RNA. There are instructions as well. Start stop, that sort of thing but it NEVER codes for proteins. The RNA is then often translated by ribosomes into proteins depending on RNA based tags or maybe at one time pure luck. It is the tags that code for TRANSLATION to DNA.

It was sloppy thinking that caused people to claim DNA coded for proteins and that sloppy thinking resulted in a lack of understanding till recently that the RNA often has biological properties without being transcribed into amino acids.

And yes that Wiki should be changed.

Ethelred
Valentiinro
not rated yet Sep 17, 2011
Okay, I changed Wikipedia. Now it says DNA codes for butts.
aroc91
1 / 5 (1) Sep 17, 2011
the genes stored in the four-letter DNA code
Not really. The Wikipedia entry "Genetic code" writes:
With some exceptions, a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid.
Additionally, it contains the RNA and DNA codon tables.


That's referring to the 4 bases, not that fact that codons are 3 nucleotides long...
4o4
not rated yet Sep 17, 2011
i agree with the whole if, should, could discussion BUT that being said, i think this is all plausible. It always kind of irked me that sympatric speciation occurs predominantly in plants.
frajo
3 / 5 (4) Sep 18, 2011
the genes stored in the four-letter DNA code
Not really. The Wikipedia entry "Genetic code" writes:
With some exceptions, a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid.
Additionally, it contains the RNA and DNA codon tables.

That's referring to the 4 bases, not that fact that codons are 3 nucleotides long...
An interesting explanation. So "four-letter words" is not referring to the length of these words but to a certain invariable set of only four letters?
Ethelred
2.3 / 5 (3) Sep 18, 2011
DNA has four nucleotide 'letters' TCGA that can form three letter long 'codons'. Each codon codes for either a bit of biological grammar or a RNA equivalent molecule, not an amino acid. Four letters by three letters long makes for 64 codons and many of the codons are redundant.

The RNA is what can code for an amino acid but RNA is not limited to being a messenger molecule. Which is why I say it is sloppy to say DNA codes for amino acids since it only codes for the RNA.

Ethelred
hush1
1 / 5 (1) Sep 18, 2011
Which is why I say it is sloppy to say...-Ethelred


In wikipedia:
http://en.wikiped...tic_code

...doesn't the first sentence only suggest the "sloppiness" (possible source of misinterpretation) you are referring to?

I can not find in the rest of the Wikipedia text a path that leads away from a straight and narrow interpretation.

Just curious.
Ethelred
2.3 / 5 (3) Sep 19, 2011
The whole thing is based on DNA as the CODE and not the storage of information that codes for RNA. ONLY RNA codes for amino acids. DNA codes for RNA. The article is written in a very standard way and that standard held up research on the activity of RNA for years.

I wrote on Apolyton.com around 2002 about RNA being largely ignored. I did that independently because not being a biologist I was not aware that a few people had recently started to look into the biological activity of RNA besides mRNA. My thinking was that the parts of DNA that coded just fine for RNA but not for functioning proteins might still be biologically active. After all it WAS active in ribosomes so why not elsewhere? And SOMETHING had to code for the ribosomes. What the hell were people thinking being so fixated on proteins?

This turns out to be true. Junk DNA is NOT all junk.

This is why all the stuff that treats DNA as coding directly for proteins needs to be replaced. The point of view is wrong.

Ethelred
Ethelred
2.3 / 5 (3) Sep 19, 2011
Taking another look at the Wiki it does have a table of RNA codons and does a proper job there. It is the intro section that behaves as if the DNA codes for amino acids. That section is what I have a problem with.

Ethelred
localcooling
1 / 5 (1) Sep 20, 2011
I think the "concept" epigenetics, is interesting as so far it is the beginning of realising that all of the cell wrapping the DNA is "epigenetics". DNA was most probably not formed "free-standing" but inside a separate "holder" or in an interactive play with such a "primitive holder".

As full-genom sequencing is getting cheaper, the realisation is coming through, that the DNA in one cell of an organism is never exactly the same as in the cell spawned off.

In spite of these differences, they are not enough to explain different behaviour between "identical" cells. Even IF the cells would have exactly the same DNA, the cell-surrounding is never the same. A cell isn't symmetrical down to atom level, and even IF it was, the likelihood that it would be split exactly in the middle is minuscule. Thus the "epigenetics" - all from methyl-groups attached directly to the DNA to molecules acting from more far away in the cell.- is what makes every "identical" cell unique.
localcooling
1 / 5 (1) Sep 20, 2011
For the sake of systematisation, everything outside the cell, shall be called (local) environment.

Small hints are arriving that some cancer might be caused by "epigenetic" changes outside of the DNA molecule but inside the cell. The term epigenetics has to be put in between citation marks, as no one knows how much of such factors are transfered almost unchanged (almost unchanged as near perfect DNA-re/duplication) to the next cell.
aroc91
1 / 5 (1) Sep 25, 2011
the genes stored in the four-letter DNA code
Not really. The Wikipedia entry "Genetic code" writes:
With some exceptions, a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid.
Additionally, it contains the RNA and DNA codon tables.

That's referring to the 4 bases, not that fact that codons are 3 nucleotides long...
An interesting explanation. So "four-letter words" is not referring to the length of these words but to a certain invariable set of only four letters?


Where are you pulling "four letter words" from? That does not exist and is not implied anywhere in this article. What you're looking for is "four letter code", which has been previously quoted and is accurate. DNA consists of 4 bases. Nowhere does that imply that codons are 4 bases long.