New limits to functional portion of human genome reported

July 14, 2017 by Jeannie Kever, University of Houston
Credit: CC0 Public Domain

An evolutionary biologist at the University of Houston has published new calculations that indicate no more than 25 percent of the human genome is functional. That is in stark contrast to suggestions by scientists with the ENCODE project that as much as 80 percent of the genome is functional.

In work published online in Genome Biology and Evolution, Dan Graur reports the functional portion of the human probably falls between 10 percent and 15 percent, with an upper limit of 25 percent. The rest is so-called junk DNA, or useless but harmless DNA.

Graur, John and Rebecca Moores Professor of Biology and Biochemistry at UH, took a deceptively simple approach to determining how much of the genome is functional, using the deleterious mutation rate - that is, the rate at which harmful occur - and the replacement fertility rate.

Both and the rate of deleterious mutations in functional parts of the genome have previously been determined, and historical data documents human population levels. With that information, Graur developed a model to calculate the decrease in reproductive success induced by , known as the "mutational load," in relation to the portion of the genome that is functional.

The functional portion of the genome is described as that which has a selected-effect function, that is, a function that arose through and is maintained by natural selection. Protein-coding genes, RNA-specifying genes and DNA receptors are examples of selected-effect functions. In his model, only functional portions of the genome can be damaged by deleterious mutations; mutations in nonfunctional portions are neutral since functionless parts can be neither damaged nor improved.

Because of deleterious mutations, each couple in each generation must produce slightly more children than two to maintain a constant population size. Over the past 200,000 years, replacement-level fertility rates have ranged from 2.1 to 3.0 children per couple, he said, noting that global population remained remarkably stable until the beginning of the 19th century, when decreased mortality in newborns resulted in fertility rates exceeding replacement levels.

If 80 percent of the genome were functional, unrealistically high birth rates would be required to sustain the population even if the deleterious mutation rate were at the low end of estimates, Graur found.

"For 80 percent of the human genome to be functional, each couple in the world would have to beget on average 15 children and all but two would have to die or fail to reproduce," he wrote. "If we use the upper bound for the deleterious mutation rate (2 × 10?8 mutations per nucleotide per generation), then ... the number of children that each couple would have to have to maintain a constant population size would exceed the number of stars in the visible universe by ten orders of magnitude."

In 2012, the Encyclopedia of DNA Elements (ENCODE) announced that 80 percent of the genome had a biochemical function. Graur said this new study not only puts these claims to rest but hopefully will help to refocus the science of human genomics.

"We need to know the functional fraction of the in order to focus biomedical research on the parts that can be used to prevent and cure disease," he said. "There is no need to sequence everything under the sun. We need only to sequence the sections we know are functional."

Explore further: Ongoing natural selection against damaging genetic mutations in humans

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betterexists
1 / 5 (2) Jul 14, 2017
Keep Going. It is Machines+Human Brain OR Machines vs. Human Brain !
Google Search Vs. Dementia/Alzheimer's. You FORGET. Google Brings it Back AT YOUR FOOTSTEPS. Software Captivated by Huge Machines!
komone
5 / 5 (3) Jul 14, 2017
This seems a little extreme. I assume they are talking about those parts that are involved in the creation of protein structures. I rather do suspect that the "junk" has an important part to play in ensuring that the "functional" parts retain integrity. Much like the host of "redundant" error correction data that protects digital data and allows your DVR to work. Why is there not even a hand-wave in this direction? Or do the authors believe that evolution would allow a baggage of maintenance for useless, energy wasting, trash DNA?
komone
1 / 5 (1) Jul 14, 2017
Further thought. If there were a "cure for cancer" then surely it would be found in some kind of dynamic maintenance of such error correction codes (ECC).
EmceeSquared
3 / 5 (2) Jul 15, 2017
betterexists:
Keep Going. It is Machines+Human Brain OR Machines vs. Human Brain !
Google Search Vs. Dementia/Alzheimer's. You FORGET. Google Brings it Back AT YOUR FOOTSTEPS. Software Captivated by Huge Machines!


You personally already lost to my Android phone's modicum of capacity. Really, your inane Phys.org rants are like Radio Free Dementia.
Ojorf
5 / 5 (3) Jul 15, 2017
I rather do suspect that the "junk" has an important part to play in ensuring that the "functional" parts retain integrity. Much like the host of "redundant" error correction data that protects digital data and allows your DVR to work.


But if that were the case, damage to the 'junk' will lead to loss of integrity of functional parts and to higher mortality, and it will by definition not be junk.
In any case this study shines a light on it from a totally different direction and your objections are included.
This is a statistical method and if damage to a gene has an effect on mortality it will show up in the numbers whether it codes for a protein or not. It just has to have an impact on mortality.
RealScience
5 / 5 (4) Jul 15, 2017
The study ignores several forms of redundancy in the genome.
For example, in trying to find the minimum viable genome numerous pairs of genes (and more complex sets) where either gene could be eliminated without any apparent consequences, but eliminating both was fatal. The non-protein-coding regions likely have similar redundancy - this would match experiments where deleting highly-conserved non-protein-coding regions had no apparent ill effect.

Also some parts of the genome may only be useful in certain unusual circumstances - if only 10% of the individuals encounter those circumstances, the impact will be only 10% as great and Graur would conclude from his statistics that only 10% of those are useful.

What Graur's statistics MIGHT show is that 10% to 15% and at most 25% of the genome is both non-redundant and important in the average individual's life.

(And there are other factors, too - essential regions are likely encoded to have lower mutation rates, etc.)
ShotmanMaslo
3.7 / 5 (3) Jul 16, 2017
Or do the authors believe that evolution would allow a baggage of maintenance for useless, energy wasting, trash DNA?


Genome sizes vary a lot between different organisms. This to me suggests that reducing genome size is not very important for survival and so yes, useless DNA would be often allowed by evolution. After all, it is still a very small part of the whole cell anyway.
Da Schneib
5 / 5 (2) Jul 16, 2017
In fact, a large amount of junk DNA is supportive of the ability to evolve. It collects mutations.

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