Dark matter made visible before the final cut

January 7, 2013
This cartoon represents alternative splicing, where an intron (in green) is potentially attached via dotted lines to exons, left and right. Credit: Zefeng Wang, PhD, UNC School of Medicine

Research findings from the University of North Carolina School of Medicine are shining a light on an important regulatory role performed by the so-called dark matter, or "junk DNA," within each of our genes.

The new study reveals of information contained in dark matter that can alter the way a gene is assembled.

"These small of tell the gene how to splice, either by enhancing the splicing process or inhibiting it. The research opens the door for studying the dark matter of . And it helps us further understand how or polymorphisms affect the functions of any gene," said study senior author, Zefeng Wang, PhD, assistant professor of in the UNC School of Medicine and a member of UNC Lineberger Comprehensive Cancer Center.

The study is described in a report published in the January 2013 issue of the journal Nature Structural & Molecular Biology.

The findings may be viewed in terms of the film industry's editorial process where snippets of celluloid are spliced, while others end up unused on the proverbial cutting room floor.

Taken from a DNA point of view, not every piece of it in each human gene encodes for a functional protein; only about 10 percent does, in coding regions called "exons." The other 90 percent of the stuff that fills the intervening regions are longer stretches of known as "introns."

But something mysterious happens to introns during the final processing of messenger RNA (mRNA), the genetic blueprint that's sent from the cell's nucleus to its protein factory. Only particular exons may be included within the final mRNA produced from that gene, whereas the introns are cut out and destroyed.

It's therefore easier to understand why more scientific attention has been given to exons. "When people are looking at the genetics of a disease, most of the time they're looking for the change in the coding sequence," Wang said. "But 90 percent of the sequence is hidden in the gene's introns. So when you study gene variants or polymorphisms that cause human disease, you can only explain the part that's in the exon. Yet the majority remains unexplainable because they're in the introns."

Following completion of the genome sequencing projects, subsequent DNA and RNA sequencing revealed the existence of more than one splice variant, or isoform, for 90 percent of human genes. During messenger RNA processing, most human genes are directed to be cut and pasted into different functional isoforms.

In a process called alternative splicing, a single gene could code for multiple proteins with different biological functions. In this way, alternative splicing allows the human genome to direct the synthesis of many more proteins than would be expected from its 20,000 protein-coding genes.

"And those different versions sometimes function differently or in opposite ways," Wang said. "This is a tightly regulated process, and a great number of human diseases are caused by the 'misregulation' of splicing in which the gene was not cut and pasted correctly."

Wang's research colleagues identified "intronic splicing regulatory elements." These essentially recruit protein factors that can either enhance or inhibit the splicing process.

Their discovery was accomplished by inserting an intron into a green fluorescent protein (GFP) "reporter" gene. These introns of the reporter gene carried random DNA sequences. When the reporter is screened and shows green it means that portion of the intron is spliced.

"The default is dark," so any splicing enhancer or silencer can turn it green," Wang explains. "In this unbiased way we can recover hundreds of sequences of inhibited or enhanced splicing."

The study collaborators put together a library of cells that contain the GFP reporter with the random sequence inserted. Thus, when researchers looking at the intron try to determine what a particular snippet of genetic information does and its effect on gene function, they can refer to the splicing regulatory library of enhancers or silencers.

"So it turns out that the sequencing element in both exons and introns can regulate the splicing process, Wang says. "We call it the splicing code, which is the information that tells the cell to splice one way or the other. And now we can look at these variant DNA sequences in the intron to see if they really affect , or change the coding pattern of the exon and, as a result, protein function."

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2.8 / 5 (9) Jan 07, 2013
So non-coding DNA had been renamed 'dark matter'?

Why? Non-coding DNA is not imaginary.
3.7 / 5 (3) Jan 07, 2013
Not only is scaffolding required to maintain the structural integrity of the DNA's shape, but also the intron substrate tilts the exon into the most desirable position for splicing, and folding, too. So long as bonding thresholds are roughly met, introns can vary subtly in structural composition and still yield the same results. They are discarded because they make no chemical contribution to protein synthesis. Inclusions in introns can cause mutations by forcing different bonding angles, so the amino acid precursor may become isomeric, or completely useless and not even get processed, such as is the case for the CCR5 allele.
2 / 5 (4) Jan 07, 2013
"Junk DNA"? "Dark matter"? Oy.

Research on this topic is interesting but the "junk DNA" term is archaic and "dark matter" is colourful language but not that enlightening (ha).
2 / 5 (1) Jan 07, 2013
I really wish they wouldn't try to equate DNA snippets that they aren't fully sure what it does to An effect that they aren't really sure what it is.

That's like trying to compare an unknown cause to an unknown effect. Opposite things.

Any issues that I have with the whole "Dark Matter" thing in itself is a whole other story.
Whydening Gyre
1 / 5 (3) Jan 07, 2013
So non-coding DNA had been renamed 'dark matter'?

Why? Non-coding DNA is not imaginary.

guess that means - neither is "dark matter". It is just stuff we either can't see or didn't consider consequential enough to matter.
1 / 5 (9) Jan 08, 2013
So it turns out that the sequencing element in both exons and introns can regulate the splicing process, Wang says. "We call it the splicing code, which is the information that tells the cell to splice one way or the other

So much for the evolutionary tale that the human genome consists mostly of inherited "leftover junk".
Since everything is turning out to be essential, there's now even less support for the imaginary evolution from some imagined ancestor.

Note the use of the words "code" and "information".

It would take a whole lot of stupendous miracles for one creature to morphs into another - no matter how long the time allocated for such imaginary process to occur.

If you do not agree - and most of this site's regular visitors will disagree, please bring documented observational evidence that one kind of organism can successfully morph into some completely different kind.
In other words - evolution [from one kind to another] has not been observed, ever. Period.

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