Having left “junk DNA” in the rearview mirror, molecular biologists are finding new treasures in the non-coding parts of the genome — creating a need for new ID-friendly metaphors.

The Action Hero with Decoder Ring

You might have to be of a certain age to remember the old TV series Jonny Quest for this metaphor: the secret decoder ring that allows you to decrypt a hidden message. This is the word picture a news item from New York University uses to describe “powers” in micro RNA.

MicroRNA can serve as a “decoder ring” for understanding complex biological processes, a team of New York University chemists has found. Their study, which appears in Proceedings of the National Academy of Sciences, points to a new method for decrypting the biological functions of enzymes and identifying those that drive diseases. [Emphasis added.]

Researchers found an easier way to decode the complex activities of enzymes that synthesize carbohydrades. “Our results show that rather than trying to trace the intricacies of this molecule’s activity, we can simply track miRNA,” says the senior author of a paper published in Proceedings of the National Academy of Sciences, because the miRNAs “illuminate which glycogenes … are vital in a biological pathway.”

The Seamstress

Clinical researchers at the University of Montreal have been studying histones, the protein machines that wrap DNA around complexes of DNA and protein called chromatin. What’s their metaphor? “This extreme compaction is made possible by proteins called histones, which condense the DNA much like thread is wound around a spool,” reducing the volume by a factor of twenty thousand. But that’s not all these threaders do; they’re also intelligent seamstresses.

Chromatin is carefully organized in such a way that genes remain “accessible” to the various proteins required for gene expression, or the interpretation of the genic information stored in DNA. Chromatin therefore provides the organism with another layer of information, referred to as epigenetic information, which is made available, in part, through specialized histones called histone variants.

The Risk-Taking Surgeon

It’s hard to know which of three metaphors to focus on in this item from Johns Hopkins. “Neurons Constantly Rewrite Their DNA,” the headline reads. But are the agents of revision (DNA regulatory tags) editors, surgeons, or risk takers? Why not all three?

Johns Hopkins scientists have discovered that neurons are risk takers: They use minor “DNA surgeries” to toggle their activity levels all day, every day….

“We used to think that once a cell reaches full maturation, its DNA is totally stable, including the molecular tags attached to it to control its genes and maintain the cell’s identity,” says Hongjun Song, Ph.D., a professor of neurology and neuroscience in the Johns Hopkins University School of Medicine’s Institute for Cell Engineering. “This research shows that some cells actually alter their DNA all the time, just to perform everyday functions.”

Later, Dr. Song says that the risky surgery is important for informational circuitry, another ID-rich word picture:

Song adds that the ability to regulate synapse activity is the most fundamental property of neurons: “It’s how our brains form circuits that contain information.” Since this synaptic flexibility seems to require mildly risky DNA surgery to work, Song wonders if some brain disorders might arise from neurons losing their ability to “heal” properly after base excision. He thinks this study brings us one step closer to finding out.

The Cook with a Scratch Pad

Try this recipe for describing epigenetics, found in an article at PhysOrg about the interaction of stresses on DNA transcription:

If DNA is the cookbook of life, then RNA is the scratch paper where the cell writes down its favorite recipes. These recipes could make the pigments of your skin, the vehicles that carry oxygen through your veins, or the signaling molecules that keep cancer in check. Sometimes, when the cell’s transcription machinery copies these recipes, it stutters or stalls, either because it gets off task or it comes across a problem with the cookbook. Then, the cell has to decide whether to keep going or give up on the recipe.

Researchers at Stowers Institute for Medical Research examined a molecule called elongin-A that can respond to stress. Normally, it keeps the transcription machinery humming along, jotting down the recipe. But when the machinery stalls, the molecule can signal disassembly of the transcription machinery. “Now, Stowers scientists and their collaborators have discovered how the molecule morphs between these two alternate identities” — prepare for two more metaphors — “one as facilitator and the other as destroyer.”

The Cowgirl

With a little poetic license, we extend the metaphor implicit in a statement from Caltech about a molecular machine (lncRNA) whose job it is “to corral and organize the proteins that are necessary for cellular processes.” And since this particular lncRNA, called Xist, is involved in silencing the extra X-chromosome in women, we didn’t want to call it a cowboy. X-chromosome inactivation is a life-or-death matter:

Researchers at Caltech have discovered how an abundant class of RNA genes, called long non-coding RNAs (lncRNAs, pronounced link RNAs) can regulate key genes. By studying an important lncRNA, called Xist, the scientists identified how this RNA gathers a group of proteins and ultimately prevents women from having an extra functional X-chromosome — a condition in female embryos that leads to death in early development. These findings mark the first time that researchers have uncovered the detailed mechanism of action for lncRNA genes.

For you cowboys out there, you’ll be pleased to hear that your shriveled-up Y-chromosome has gotten a little more respect recently. Science Daily reports that in animals that have lost their Y, the genes merely relocated to other chromosomes. This proves they are still essential. That’s why the article is about “Why the Y Genes Matter,” even though the human male Y-chromosome is much smaller than the X. It’s not the years; it’s the mileage.

From Dead Junk to Live Actors

Threaders, surgeons, editors, risk takers — these metaphors reflect the growing picture of non-coding DNA as alive and active in the genome. True, every so often, you find researchers unwilling to jettison the Darwinian thinking that led to the junk-DNA myth in the first place. It’s an exciting time, though, to see such progress, reflected in ID-friendly metaphors that are fast coming to replace the dismissive “junk” label.

Image: � Maya Kruchancova / Dollar Photo Club.