A Genome Without the Junk Proves that ENCODE Conclusions are Garbage

One of the shocking results of the Human Genome Project was the finding that we only have about 20 thousand genes. This seemed a ridiculously small number to encode an organism as complex as a person. How does a fertilized egg turn itself into an adult human being when it is only equipped with some 20 thousand genes in its nucleus to guide the process??

You might think that if people have 20 thousand genes then other organisms must have far fewer. We’re better than them, right? You’d think it would take more genes to make a person than a mouse, or a frog, or a fruit fly. But it turns out that all mammals have pretty much the same number of genes. And many amphibians have more genes than us. And fruit flies have about 15 thousand genes, a number not way different from us. It is clear that we are not at the apex of the chart when it comes to gene number.

It turns out that only about one percent of our DNA is encoding protein, the prime function of genes. The proteins are the workers, making muscles move, breaking down food, creating energy, and building the backbones of our cells. DNA is the sacred data storage unit, passed from one generation to the next, carrying the code that tells cells how to make proteins. But if genes make up only one percent of our DNA, then what does the rest of the DNA do??

There are competing theories. Some scientists say most of this extra DNA is just junk. It exists, but it does no harm, and we live with it. It is excess baggage that we carry around. But others contend that most DNA actually has function, perhaps in creating very fine regulatory networks to make sure that the genes are properly expressed.

To better understand the function of the noncoding DNA the US National Institutes of Health funded the ENCODE project, the Encyclopedia of DNA Elements. Hundreds of scientists were put on the job, hundreds of millions of dollars were spent, and some of the results have now been published in the most prestigious journals. They were looking for the function of this extra DNA, and they loudly proclaimed that they had indeed found it. And it was not junk! Indeed, based on their studies they concluded that at least 80% of the DNA, not just the 1% encoding proteins, has important function in at least some cell type.

So, one might think, problem solved.

But then an international consortium of 29 scientists published a study of a rather remarkable plant, U. gibba. They are bladderworts, often compared to snapdragons and orchids, and they are carnivorous, trapping and digesting prey organisms. It turns out that U. gibba has a very surprising genome, with almost no junk DNA. The results were so unexpected that the paper was published in Nature (June 2013), one of the most prestigious journals. It turns out that the U. gibba DNA has 28,500 genes, significantly more than human DNA, but the total amount of DNA per cell is only 77 megabases, about 40 times smaller than ours. So, while there are far more protein encoding genes, there is far less DNA. There is almost no junk!

And it is not something peculiar to plants. Most plant DNAs are like most animal DNAs, with only a very small percentage consisting of genes. An evolutionary comparison of the U. gibba DNA with DNAs from related plants, including tomatoes and snapdragons, shows that the U. gibba has somehow figured out how to eliminate the excess DNA. And yet is does just fine! It doesn’t need the junk!

The unavoidable conclusion is that the extra DNA is not required. It has no essential function. It is really just junk. And ENCODE is wrong.

6 thoughts on “A Genome Without the Junk Proves that ENCODE Conclusions are Garbage

  1. WOW, this is very interesting. I’m sure there will come a day when we REALLY have this down and we’ll be able to shed all excess DNA baggage before we start tweaking ourselves into the perfect organism.

    • We are pretty good at manipulating the mouse genome right now. It would be interesting to see what would happen if we took out the “junk” DNA. Could we make a junkless mouse?? But there is a lot of junk to remove, so it would be a very long and expensive project.

  2. The most important function of non-coding DNA (“introns”) is to determine when and where the coding DNA (“exons”) gets transcribed. Different gene expression in different cells at different times is what controls our metabolisms, what makes us hum.

    Plants have fewer cell types and less complex anatomy, so they need less complex gene expression control systems. I’m guessing that bladderworts might have simple structures with fewer cell types than most plants. It doesn’t help my theory much that bladderworts are carnivorous. http://en.wikipedia.org/wiki/Utricularia

    • This is a reasonable line of thought. But it turns out that plants in general have as much noncoding (introns and intergenic) DNA as animals. And, as you point out, this carnivorous plant is not especially simple. There are close relative of this plant that have lots of noncoding DNA. At the very least one can conclude that these relatives have DNA they don’t need. I prefer the more general conclusion that this plant figured out a way to get rid of the excess baggage, and most noncoding DNA, for other species as well, is in fact not functional. Of course, as you point out, some of it is indeed regulatory and performs a critical function. But do we really need a hundred times more noncoding DNA than coding? I doubt it.

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