How much of your DNA is functional?

November 14, 2014 by Ella Kelly

(Phys.org) —The human genome consists of six billions rungs of DNA – but how much of this DNA is actually doing anything important?

Two years ago research emerged that suggested that a large proportion of DNA, 80 percent, was functional. This figure came from interpretations of research conducted by the Encyclopedia of DNA Elements (ENCODE).

This estimate was almost immediately taken up by and received a lot of media attention, as well as backlash from other geneticists including Dr. Dan Graur who called the findings "absurd".

Now a new study, lead by Dr. Gerton Lunter from the University of Oxford's Wellcome Trust Centre for Human Genetics in the UK, has instead found that only 8.2 percent of human DNA is functional.

Yes, a jump from 80 to 8.2 percent seems a bit extreme – and you may be asking how these two research groups came to such drastically different conclusions? As University of Melbourne researcher Dr. Charles Robin explains, the disparity lies in the definition of the term "functional".

ENCODE defined functional as a "biochemical function" – meaning that if a section of DNA is transcribed or bound by particular proteins, it would be termed "biochemically functional", even if it did not have any eventual impact on the individual's phenotype.

How much of your DNA is functional?

It was this version of functional that lead to the large estimation of 80%. However, many researchers, including Dr. Graur and Dr. Robin, disagree with this definition of function.

Dr. Robin instead suggests the term "functional" should be used to denote sections of DNA that, if disrupted, would have harmful effects, therefore making these sections of DNA critical to development – and this is the definition used by Dr. Lunter and his colleagues in their recent study.

To test this a geneticist could purposely delete sections of the DNA and examine the impact on fitness. However, there are obvious ethical limitations for doing this in humans.

Instead, Dr. Lunter and his research group examined the disruptions generated by evolution to assess what parts of DNA are functional. Essentially, those sequences that were most unchanged, or conserved, are likely to have a function, while those without function evolve over time without any constraints.

The researchers looked at a range of species that all had different levels of divergence from humans. The functional part of the genome has changed over evolutionary time as species diverged, leading to phenotypic evolution that causes a human to look different to a mouse. Lunter and colleagues quantified these differences between and the genomes of species of various evolutionary distances to arrive at their estimate of 8.2 percent.

"The figure of 8.2 percent is not surprising," said Dr. Robin. "It is what we would expect based of previous research. The great thing about this paper, however, is the quantitative methods that have now given us a clearer answer."

These results will not only have significant implications for genetics research, but also will become important for a number of other fields, such as medical research.

When using mice models, knowing the differences in functional genes between mice and humans will help medical researchers understand how humans may react differently to mice in medical studies.

The next step for researchers will be to determine the purpose and function of this important 8.2 percent of DNA.

And what about the other 91.8 percent?

Surprisingly, the rest of the DNA is mostly useless, and although there may be genes in there that encode interesting elements, research will focus first on uncovering the secrets of that small, but important, 8.2 percent of functional DNA.

Explore further: 8.2 percent of our DNA is 'functional'

More information: Rands CM, Meader S, Ponting CP, Lunter G (2014) "8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage." PLoS Genet 10(7): e1004525. DOI: 10.1371/journal.pgen.1004525

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eric96
1 / 5 (5) Nov 14, 2014
100% of DNA has a function
Perhaps 8% active and 92% standby, but 100% of DNA has a function.
Let us consider what gets "saved" and encoded into DNA.
Even DNA is a finite storage source, so only selected "memories" are saved.
If the majority of the "memories" were bad, then we would in much rougher shape.
So clearly the invisible intelligence of life makes mostly correct decisions, say, roughly 90% correct. Well if that's true and it must be true otherwise we would have a far shorter life span (we have a long one compared to most mammals), then 100% of DNA must have a function aka "memory", whether only 90% of that is good or whatever the ratio, is not the question, all of it has a function. So what does 92% of Idle dna do. It's mostly circumstantial; environment triggers (internal and external) so that we can adapt internally to varying environments and externally so we can adapt mentally and physically, to survive and thrive.

eric96
1 / 5 (5) Nov 14, 2014
Think about rats, 99.999% percent of them just went on with their rat life.
But 1 rat was special, had some kind of brain beyond basic instinct and thought
"I could be much safer if I could see my enemies from a distance"
So the rat started to stand, and look.
And this rat had 8 babies which learned the same behavior.
Eventually this behavior was encoded into dna.
And somehow through some divinity, God said let the rat stand.
But still at a limited height rats were unsatisfied.
So they constantly tried to see higher, and slowly, over time, they grew taller.
And a human was born.
We have no primate origin.
We are rats, thru and thru.
JVK
1 / 5 (5) Nov 14, 2014
http://www.plosge....1004525

"The class of functional element inferred to turnover fastest was that of lncRNAs, again consistent with observations that most human lncRNAs are primate-specific and only 19% of lncRNAs are conserved over more than 90 My [33]."

Nutrient-dependent changes in the microRNA/messenger RNA balance are the link between the epigenetic landscape and the physical landscape of DNA in the organized genomes of species from microbes to man in my model.

RNA-mediated amino acid substitutions differentiate cell types via the de novo creation of olfactory receptor genes linked from nutrient uptake to pheromone-controlled physiology of reproduction in insects and mammals.

http://www.ncbi.n...24693353

The molecular epigenetics that link physics to the chemistry of protein folding are not likely to change across species merely because evolutionary theory requires mutations.
FainAvis
not rated yet Nov 14, 2014
"Now a new study, lead by Dr. ..." To all you people who are not native English speakers: There are times when one should say 'led', and this is one of them.
The article should say: "Now a new study, led by Dr. ..."
JVK
1.7 / 5 (6) Nov 14, 2014
Journal article excerpt: "...two mammalian hypothalamic enhancers have no homolog across non-mammalian vertebrates, yet are still able to drive specific expression patterns in zebrafish neurons [37]. These findings are consistent with gene expression evolution being shaped predominantly by stabilizing selection on the expression level [38], while evolution on the sequence level may involve an interplay between fixation of weakly deleterious mutations through drift, and weak positive selection on compensatory mutations [39]."

The findings are consistent with effects of the concentrated yeast alpha mating pheromone on cultured pituitary cells of rats that release luteinizing hormone, which is typically modulated by GnRH.

Substitution of glycine, which is the only achiral amino acid, in the GnRH molecule appears to have stabilized the organized genomes of all vertebrates. I cannot imagine how mutations could do what amino acid substitutions obviously do.
JVK
1.7 / 5 (6) Nov 14, 2014
Less than 10% of human DNA has functional role, claim scientists
http://www.thegua...-baggage

Excerpt: "Evolution can tell you whether something is important or not important, but it doesn't tell you what that something actually does," he added."

My comment: Nutrient-dependent amino acid substitutions link RNA-mediated events from ecological variation to ecological adaptations via conserved molecular mechanisms in species from microbes to man.

That tells you exactly what the amino acid substitutions do and how they do it. They stabilize DNA in organized genomes and link epigenetic effects on the biophysically constrained chemistry of protein folding to cell type differentiation that is perturbed by mutations.

If not for the pseudoscientific nonsense of evolutionary theory, others might have learned to incorporate physics and chemistry into accurate representations of cause and effect.
Captain Stumpy
5 / 5 (5) Nov 15, 2014
cell type differentiation that is perturbed by mutations
@
I cannot imagine how mutations could do what amino acid substitutions obviously do
you moron
your own model causes mutations so either you are truly stupid or you are simply pushing a KNOWN PSEUDOSCIENCE because your FAITH demands it
remember.. I asked
DOES your model make any changes to the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element?
This is a yes or no answer
(this is the DEFINITION of mutation) to which you answered
YES!
--Thanks for asking
you are WRONG regarding mutations and your own model supports the theory of EVOLUTION, which is supported by science and fact, not a wanna-be diagnostician who failed college and is a glorified lab tech who LIES about his diagnostic abilities (sans License) to bolster his authoritarian image with himself

Mike_Massen
4.4 / 5 (7) Nov 15, 2014
JVK claimed
If not for the pseudoscientific nonsense of evolutionary theory, others might have learned to incorporate physics and chemistry into accurate representations of cause and effect.
Please clarify this odd phraseology - is english your first language ?

What theory is present which is credible rival please JVK - url ?

Any evidence which supports that un-named theory - url ?

Does it go some way to (Eg.) offer a suggestion how the commonly observed feature of matter self-assembling (such things as protons/e- to atoms to molecules etc) & what artifact of advanced probability may be imperative in the arrangement of amines into RNA/DNA ?

ie. There is evidence early earth's atmosphere had NH3, CO, CO2, H2O etc with propensity to generate formamide which given time & heat (in abundance) produces Guanine - ie A DNA base pair.

Does this un-named rival theory show probabilistic base go beyond that somehow other than chemico-evolutionary processes already used ?
imido
Nov 15, 2014
This comment has been removed by a moderator.
rgw
3 / 5 (2) Nov 15, 2014
The simple answer is, All of it.
JVK
1 / 5 (4) Nov 15, 2014
...what artifact of advanced probability may be imperative in the arrangement of amines into RNA/DNA ?


Thanks for asking. The probability that life is nutrient-dependent can be linked from amino acid substitutions via biophysically constrained protein folding, which is controlled by the metabolism of the nutrients to species-specific pheromones. The pheromones control the physiology of reproduction, which means they link fixation of the amino acid substitutions in the organized genomes of species from microbes to man to ecological variation and ecological adaptations via ecological speciation.

What theory is present which is credible rival please JVK - url ?

Any evidence which supports that un-named theory - url ?


No theory, just a model with across-species evidence based on experimental results, not theory. See for examples: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353
Captain Stumpy
5 / 5 (4) Nov 15, 2014
No theory, just a model
@jk
your crusade against mutations should include your own model, moron, because even YOU admitted your model causes mutations
DOES your model make any changes to the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element?
This is a yes or no answer
(this is the DEFINITION of mutation) to which you answered
YES!
--Thanks for asking
so your constant posts against mutations and your derision of modern scientists for being able to read and comprehend the lexicon of the field you chose to be a part of is simply your own feeble attempts to mask your low self esteem and past failures

when are you going to stop posting kohl-slaw word salads which obfuscate science and reality and just get on with it?
you act like English is a fourth language and you are illiterate
quit trying to punch up your posts with a thesaurus and learn a little about reality

jvk=PSEUDOSCIENCE TROLL!
JVK
1 / 5 (4) Nov 15, 2014
when are you going to stop posting kohl-slaw word salads which obfuscate science


If ever I quit finding scientific support for my accurate representations, which link physics and chemistry to biology via the conserved molecular mechanisms of nutrient-dependent cell type differentiation, I will stop trying to explain links to the nutrient-dependent physiology of reproduction in terms that serious scientists understand.

I can then be like Captain Stumpy who ignores anything that does not seem to fit into the context of what he was taught to believe -- no matter how ignorant what he was taught has made him.

See for example: ""The holy grail is to find that quantum effects stimulate biological processes that are relevant to medicine," says Al-Khalili." http://discoverma...tum-life

The holy grail is de novo creation of olfactory receptor genes in vertebrates and invertebrates, which is linked to all other species via quantum effects.
russell_russell
3 / 5 (4) Nov 16, 2014
All definitions are tautologies.
All definitions are place holders.
All definitions become obsolete and superseded.
The evolution of language guarantees this.

The author of the article is seeks readers.
I cannot imagine how mutations could do what amino acid substitutions obviously do. JVC


You are in the best of company. No one can. Why? Mutations do not do what amino acid substitutions do. Obviously.

With your "accurate representation" (model) you up the ante.
What ante? You start with a superseded and obsolete model that explains less the more the passage of time presents evidence to the contrary. Why stop there?
You up the ante further and state:
What evidence?
Your references to current literature are valuable. Your assertions claiming the references cited lending support to your model are fatal. Have any of authors of the cited research thanked you for having unified evolution, biodiversity, and cell differentiation under your model?
JVK
1 / 5 (4) Nov 16, 2014
Have any of authors of the cited research thanked you for having unified evolution, biodiversity, and cell differentiation under your model?


Thanks for asking. Elekonich and Robinson (2000) used our 1996 model of RNA-mediated events in their representation of hormone-organized and activated behavior in insects and "Amino Acid Residues Contributing to Function of the Heteromeric Insect Olfactory Receptor Complex" http://dx.doi.org....0032372 extended the life history transitions across other species.

Finally, however, works from Vosshall's group can be paired with "Experimental Food Restriction Reveals Individual Differences in Corticosterone Reaction Norms with No Oxidative Costs" http://dx.doi.org....0110564 This links nutrient uptake to amino acid substitutions and pheromone-controlled chromosomal rearrangements in birds.

"Role of olfaction in Octopus vulgaris reproduction" cites Kohl (2013)

JVK
1.8 / 5 (5) Nov 16, 2014
http://www.scienc...14004006

"...olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000)."

Hold the applause.

Although there is no other model for comparison, no one dares call too much attention to their own works by commenting directly on the fact that my works link microbes to man via conserved molecular mechanisms. They don't want to invite the wrath of the ignorant theorists and, with few exceptions, they want to claim that they were the first to discover a piece of the puzzle, which obviously must link physics, chemistry, and biology as we did in "From fertilization to adult sexual behavior" via the conserved molecular epigenetics we detailed. http://www.hawaii...ion.html
Da Schneib
5 / 5 (4) Nov 20, 2014
Aside from the parts of DNA that are evolutionarily conserved, it's important to note how much of it gets expressed and how much acts as regulation sites. I think these two questions will separate the wheat from the chaff.

But looking at it from an evolutionary point of view, the correct answer is, "all of it." Our DNA contains most of a billion years' worth of solutions to various types and levels of problems. Who could ever predict what the next "right answer" will be to adapt to the ever-changing environment? So, better keep a lot of "right answers" handy to try out in an emergency; which is exactly how evolution by selection works. DNA is a device for conserving mutations. When life evolved the ability to evolve, that is the constant gene-mixing of sexual reproduction, and added it to the ability to conserve mutations for later expression, that's when it really took off.
russell_russell
5 / 5 (2) Nov 20, 2014
Expressions are regulation. Why stop there?
All expression is sourced from the repair of damage - the first and foremost mechanism for evolution, biodiversity and cell differentiation.
"Conserved mutations" is nothing more than repair. To have a mutation you need damage.
No cell escapes damage. Every one of your cells carries out repair an average of sixty thousand times a day.
Da Schneib's "right answer" is repair. Permanent repair. Why stop there? Neurons use temporary repair. Because that's what learning and memory essentially is - repair of damage - sixty thousand times a day for every neuron of every form of life processing neurons.
Yes, "DNA is a device for conserving mutations." Why stop there? DNA is a device to store any learning process as memory.

"When life evolved the ability to evolve" [the synonyms for the word 'repair'] "that is the constant gene-mixing of sexual reproduction" [the synonyms for the replication of repair]
cont...

russell_russell
5 / 5 (3) Nov 20, 2014
cont...
"...and added this the ability to conserve mutations for later expression " [again synonyms for permanent repair passed on], "that's when it really took off." [the beginning and origin of life]

No repair, no life.
http://medicalxpr...ain.html

It's that simple. It's that robust. It has to be - to withstand an unpredictable environment.

Da Schreib and I are literally on the same page, same book, same author.

JVK is still reading the Grimm brothers.
JVK
1 / 5 (2) Nov 20, 2014
Grimm brothers?

Enhanced Transcriptome Maps from Multiple Mouse Tissues Reveal Evolutionary Constraint in Gene Expression for Thousands of Genes http://www.biorxi...0/010884

How can DNA stability and DNA repair not be linked via the conserved molecular mechanisms of nutrient-dependent RNA-mediated cell type differentiation, which is involves amino acid substitutions?

Is that what you think is akin to the Grimm Brother's stories?

"DNA is a device for conserving mutations."
What kind of idiot makes claims like that?

(That was a rhetorical question.)

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