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Thursday, March 05, 2015

Garbage, Junk, and non-coding DNA

About 1% of the genome codes for actual proteins: these regions are the ~20k or so "genes" that receive most of the attention. (Usage of the term "gene" seems to be somewhat inconsistent, sometimes meaning "unit of heredity" or "coding region" or "functional region" ...) There's certainly much more biologically important information in the genome that just the coding regions, but the question is how much? One of the researchers below estimates that 8% is functional, but it could be much more.

See also Adaptive evolution and non-coding regions.
NYTimes: Is Most of Our DNA Garbage?

... Rinn studies RNA, but not the RNA that our cells use as a template for making proteins. Scientists have long known that the human genome contains some genes for other types of RNA: strands of bases that carry out other jobs in the cell, like helping to weld together the building blocks of proteins. In the early 2000s, Rinn and other scientists discovered that human cells were reading thousands of segments of their DNA, not just the coding parts, and producing RNA molecules in the process. They wondered whether these RNA molecules could be serving some vital function.

... In December 2013, Rinn and his colleagues published the first results of their search: three potential new genes for RNA that appear to be essential for a mouse’s survival. To investigate each potential gene, the scientists removed one of the two copies in mice. When the mice mated, some of their embryos ended up with two copies of the gene, some with one and some with none. If these mice lacked any of these three pieces of DNA, they died in utero or shortly after birth. “You take away a piece of junk DNA, and the mouse dies,” Rinn said. “If you can come up with a criticism of that, go ahead. But I’m pretty satisfied. I’ve found a new piece of the genome that’s required for life.”

... To some biologists, discoveries like Rinn’s hint at a hidden treasure house in our genome. Because a few of these RNA molecules have turned out to be so crucial, they think, the rest of the noncoding genome must be crammed with riches. But to Gregory and others, that is a blinkered optimism worthy of Dr. Pangloss. They, by contrast, are deeply pessimistic about where this research will lead. Most of the RNA molecules that our cells make will probably not turn out to perform the sort of essential functions that hotair and firre do. Instead, they are nothing more than what happens when RNA-making proteins bump into junk DNA from time to time.

... One news release from an N.I.H. project declared, “Much of what has been called ‘junk DNA’ in the human genome is actually a massive control panel with millions of switches regulating the activity of our genes.” Researchers like Gregory consider this sort of rhetoric to be leaping far beyond the actual evidence.

... Over millions of years, essential genes haven’t changed very much, while junk DNA has picked up many harmless mutations. Scientists at the University of Oxford have measured evolutionary change over the past 100 million years at every spot in the human genome. “I can today say, hand on my heart, that 8 percent, plus or minus 1 percent, is what I would consider functional,” Chris Ponting, an author of the study, says. And the other 92 percent? “It doesn’t seem to matter that much,” he says. ...


efalken said...

This is a puzzle. ENCODE found 80% of DNA is transcribed, which would suggest a massive waste of energy if only 10% of that is actually functional. 80% vs. 8% depends on whether you think pseudogenes or transposons are usually or rarely functional. We will find out, but if it is more like 80% functional it is important and we do not understand how DNA really works, especially as these 'junk' regions seem to have so much random variation. I get the sense there's a lot feedback and redundancy in gene expression regulators.

Iamthep said...

It would seem that non conserved regions of DNA would not be functionally relevant in the sense that they control expression or creation of proteins, or even of RNA.

But perhaps they are important in a mechanical sense. DNA is would up awfully tight in the nucleus wrapped around histones. It seems to me that if there was no dead space then it might be hard to read/express all the needed sections of DNA in order to function properly. Though I have never really learned exactly how cells deal with unwrapping DNA from histones when needed.

BobSykes said...

I agree with efalken, energy considerations alone suggest that most, if not all, DNA has some function. The idea that there is such a thing as junk DNA is the sibling of the ideal that we only use 10% of our brain. Both statements are measures of our ignorance.

JayMan said...

Very well said.

kurt9 said...

Both viewpoints are likely correct. Some of the non-coding DNA serves a regulatory environment. But not all of it. Some of it may well be vestigial artifact of evolution. I think some of it is simply built-in redundancy. One thing that is very clear about molecular biology is its redundancy.

Bibibibibib Blubb said...

They have deleted pretty chunks of junk dna in mice with very little to no effect. They even deleted stuff that they thought would be most likely to be functional.



DK said...

This is a puzzle only for those who do not understand biochemistry. Those who do know that ENCODE amplified white noise.

Emil Kirkegaard said...

The genome often contains alternatives for some specific protein. So sometimes one can remove the DNA that codes for one of these, which means that the body will switch to using the other.

JayMan said...

So what do you think of this?

PLOS Genetics: The Case for Junk DNA

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