'Junk' DNA reveals vital role [ultra-conserved sequences]

Nature Magazine ^ | 07 May 2004 | Helen Pearson

[PatrickHenry]

If you thought we had explored all the important parts of our genome, think again. Scientists are puzzling over a collection of mystery DNA segments that seem to be essential to the survival of virtually all vertebrates. But their function is completely unknown.

The segments, dubbed 'ultraconserved elements', lie in the large parts of the genome that do not code for any protein. Their presence adds to growing evidence that the importance of these areas, often dismissed as junk DNA, could be much more fundamental than anyone suspected.

David Haussler of the University of California, Santa Cruz, and his team scanned the genome sequences of man, mouse and rat¹. They found more than 480 ultraconserved regions that are completely identical across the three species. That is a surprising similarity: gene sequences in mouse and man for example are on average only 85% similar. "It absolutely knocked me off my chair," says Haussler.

The regions largely match up with chicken, dog and fish sequences too, but are absent from sea squirt and fruitflies. The fact that the sections have changed so little in the 400 million years of evolution since fish and humans shared a common ancestor implies that they are essential to the descendants of these organisms. But researchers are scratching their heads over what the sequences actually do.

The most likely scenario is that they control the activity of indispensable genes. Nearly a quarter of the sequences overlap with genes and may be converted into RNA, the intermediate molecule that codes for protein. The sequences may help slice and splice RNA into different forms, Haussler suggests.

Another set may control embryo growth, which follows a remarkably similar course in animals ranging from fish to humans. One previously identified ultraconserved element, for example, is known to direct a gene involved in the growth of the brain and limbs.

To solve the conundrum, experts predict a flurry of studies into the enigmatic DNA chunks. "People will be intrigued by this [finding]," says Kelly Frazer who studies genomics at Perlegen Sciences in Mountain View, California. "It is the kind of stuff that blows people away."

Hard to believe

Geneticists have known for some years that there are critical sections of DNA aside from the much-acclaimed genes. A fair fraction of the mouse and human genomes, aside from protein-coding sequences, show strong similarities.

But ultraconserved segments are particularly unusual because they are 100% identical in man and mouse. Until now, some thought they were human DNA that had contaminated mouse samples. "People had a hard time believing it," Frazer says.

The presence of exact copies in different animals suggests that even tiny changes in the sequence of these segments destroy whatever they do, and have been weeded out during evolution. Non-essential regions of DNA, by contrast, tend to accumulate mutations so that the sequences vary in different organisms.

Figuring out what the mystery segments do will be difficult. There are few similarities between one region and another, so these cannot be used to provide clues to their function. One laborious technique will be to genetically engineer mice that lack one segment and see how that affects their growth and behaviour.

Once the function of ultraconserved elements is resolved, researchers will still have to tackle other vast tracts of the genome that are similar in different organisms, says geneticist Kerstin Lindblad-Toh of the Broad Institute in Cambridge, Massachusetts. "This is the tip of the iceberg," she says.

[PatrickHenry]

One might even get the idea that -- gasp! these different species were all related.

Footnote's text and a worthless graphic in original article.

Another article on this subject: Surprising 'Ultra-conserved' Regions Discovered In Human Genome.

[PatrickHenry]

PING. [This list is for the evolution side of evolution threads, and some other science topics like cosmology. FReepmail me to be added or dropped. Long-time list members get all pings, but can request evo-only status. New additions will be evo-only, but can request all pings. Specify all pings or you'll get evo-pings only.]

[HiTech RedNeck]

The fact that the sections have changed so little in the 400 million years of evolution since fish and humans shared a common ancestor implies that they are essential to the descendants of these organisms.

Or could it be the flourish in God's "John Hancock" eh???

[anobjectivist]

That's really cool.

I wonder what that DNA does.

[Maurice Tift]

One laborious technique will be to genetically engineer mice that lack one segment and see how that affects their growth and behaviour.

[aruanan]

One might even get the idea that -- gasp! these different species were all related.

No one's ever doubted that except for those who postulate separate instances of spontaneous biogenesis.

"This is the tip of the iceberg," she says.

And the tip of the RO1s.

[Junior]

TUCvER bump (yep, I'm putting a new one together...)

[Pharmboy]

When this stuff was first discovered ("introns" and "exons" were the terms used to differentiate the structural genes from the "junk"), I remember scientists saying it had no function; I thought to myself that these people do not understand evolution. They do not know that biosystems do not expend energy on crap.

It was just a matter of time until findings like this came about, and eventually a purpose will be found.

[glock rocks]

ping

[TigerLikesRooster]

Re #5

Don't forget the pair below.

[alloysteel]

What if we have just discovered where the soul resides? You know, that inner spark that transcends death, and may or may not be reborn in a new incarnation.

[AntiGuv]

You think mice and rats have souls?

[alloysteel]

"You think mice and rats have souls?"

Sure. Small and stunted, to be sure, but if the belief in reincarnation is explored a little further, it would be entirely consistent with souls being punished for having lived a less than illustrious lifetime. A couple stints in the short unhappy life of a rodent would be expected to stamp out arrogance and instill a little humility, at which time the soul would be permitted to be reborn as, say, a creature that preyed on rodents, like a rat terrier or a tough mouser cat.

[NonValueAdded]

What about the Ultra-Progressive regions? _{I know it says conserved and not conservative but admit it, doesn't the word grab your attention? Let's see whose sense of humor is working this Monday AM}

[AntiGuv]

OK, thanks! Interesting idea.

[buffyt]

I see this as PROOF that evolution is a big lie.

In the beginning, God CREATED....

NOT

In the beginning, evolution just happened for no reason no plan no design..... just POOF! there was the earth and life just evolved for no reason ..... LOL

[Shryke]

I see this as PROOF that evolution is a big lie.

Wow! Seriously, have you ever not come to that conclusion?

In the beginning, evolution just happened for no reason no plan no design..... just POOF! there was the earth and life just evolved for no reason ..... LOL

The only thing laughable about that statement is your assertion that evolution tries to explain life's origin. Sorry, it doesn't. Why are some creationists unable to grasp this very simple fact?

[Chewbacca]

I bet they find out these things are their for error checking the DNA and make sure that any mutations are rendered sterile.

[KellyAdmirer]

I never for a second believed that those long stretches of "junk" DNA were anything of the kind, such waste made no sense at all, but the professors all passed it off as if it were the Gospel truth....

[aculeus]

Calling these genes "junk" was stupid. It was someone's hypothesis (that they had no function) and everyone bought it ... at least the name was quickly accepted.

They were always "mystery" genes or UGM (unidentified genetic material) but "junk" was a totally unjustified conclusion.