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Discoveries Make the "Junk DNA" Rubble Bounce


"Junk DNA" is the first phrase in the headline of an article at Science Daily, " 'Junk DNA' Made Visible Before the Final Cut," but the news being reported in fact has to do with an exquisite design in what was formerly thought to be junk.

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 findings are reported in Nature Structural & Molecular Biology ("A complex network of factors with overlapping affinities represses splicing through intronic elements").

If it's "so-called" junk, whoever is calling it that is wrong. An "important regulatory role" is not a junk job, unless it's being done by an incompetent government employee.

The article describes roles for alternative splicing, where elaborate molecular machines in the nucleus rearrange snippets of DNA code into a variety of RNA transcripts, allowing multiple functional products to come from the same DNA. Geneticists have long been so focused on the exons that become protein-coding RNA's that they have failed to appreciate what the introns are doing. Introns are snippets of DNA that are spliced out of the messenger RNA (mRNA) before it goes to the ribosome for translation into protein. They once appeared to be leftovers on the cutting room floor, but have turned out to be essential.

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.
While not ending up as part of a messenger RNA, introns regulate what goes into the "final cut." The team in the editing room is just as important as the actors on the screen. Now they're not just introns (intervening stuff); they are intronic splicing regulatory elements: "These essentially recruit protein factors that can either enhance or inhibit the splicing process." Lead author Zefeng Wang even drew a cartoon analogy that shows how different sentences can be spliced from individual words (exons), depending on how the "splicing code" (including introns) rearranges them.
"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 splicing, or change the coding pattern of the exon and, as a result, protein function."
Meanwhile a news release from the Research Institute of Molecular Pathology in Vienna mentions junk DNA, only to immediately correct the misnomer:
Genome sequences store the information about an organism's development in the DNA's four-letter alphabet. Genes carry the instruction for proteins, which are the building blocks of our bodies. However, genes make up only a minority of the entire genome sequence -- roughly two percent in humans. The remainder was once dismissed as "junk," mostly because its function remained elusive. "Dark matter" might be more appropriate, but gradually light is being shed on this part of the genome, too.
It's not even dark matter either, though, if you can shed light on it and see things at work. In fact, the "dark matter" looks to be just as important as the code itself:
Far from being useless, the non-coding part of DNA contains so-called regulatory regions or enhancers that determine when and where each gene is expressed. This regulation ensures that each gene is only active in appropriate cell-types and tissues, e.g. haemoglobin in red blood cell precursors, digestive enzymes in the stomach, or ion channels in neurons. If gene regulation fails, cells express the wrong genes and acquire inappropriate functions such as the ability to divide and proliferate, leading to diseases such as cancer.
The article goes on to describe what the IMP team found these regulatory regions doing, by employing new tools they intelligently designed to monitor the action. They watch them enhancing the rate of transcription of some genes. They see others do housekeeping. "In addition, they find several enhancers for each active gene, which might provide redundancy to ensure robustness of gene regulation."

That's not junk. The only thing that's garbage here is the term "junk" itself. Let's give due credit to these hard-working regulators that keep our intelligently designed bodies running smoothly (most of the time).

Image: NobMouse/Flickr.