New classes of RNAs emerge as key players in the brain

RNA compels Georges St. Laurent III to go to the gym. The genetic molecule inspires him to eat right and take care of himself. His efforts are all aimed at maintaining the delicate machinery housed in his cells.

iStockphoto/S. Norcross

DATA PROCESSORS. Noncoding RNA molecules are versatile conveyors of information in cells and can carry both analog and digital messages. M. Mazaitis

But while he cares for his body, it’s the supercomputer in his brain he’s really trying to preserve. After all, the human brain is evolution’s finest achievement, says St. Laurent, a computational and molecular biologist at George Washington University in Washington, D.C. And while many have focused on the import of DNA’s genetic information, he believes that DNA’s chemical cousin, RNA, is the true hero.

“All of the finer capacities that we have—to play an instrument, make art, do science” we owe to RNA, St. Laurent says. “If we didn’t have these little RNAs floating around [in the brain], we wouldn’t be able to remember mathematics or color patterns.”

Many people regard ribonucleic acid, as RNA is formally known, as “just a middleman between DNA and protein,” says Claes Wahlestedt, a neuroscientist and genome researcher at the Scripps Research Institute in Jupiter, Fla. Shuttling genetic information from DNA to a cell’s protein factories has long been recognized as RNA’s day job, summarized in the mantra that “DNA makes RNA makes protein.” Historically, RNAs that don’t encode proteins have gotten about as much respect as Rodney Dangerfield.

In recent years, though, scientists have discovered an extended family of RNA molecules that perform various crucial jobs in the cell’s information technology department. In fact, Wahlestedt, St. Laurent, and a growing number of other researchers think that noncoding RNAs hold the information necessary to create and maintain human brains. Without noncoding RNA, the human brain would be unthinkable, St. Laurent says.

The human brain is dynamic, containing roughly 100 billion neurons, each one with up to 100,000 synapses connecting it to other neurons.

“All those synaptic connections are constantly being remodeled by environmental interactions,” says Mark Mehler, a clinical neurologist and molecular biologist at Albert Einstein College of Medicine in Bronx, N.Y. “Every millisecond of your life you have millions and billions of sensory inputs” converging on the brain.

Mehler has devoted himself to understanding how the brain works and learning to fix it when it breaks down. He long ago decided that the only way to heal an ailing brain is to coax specialized stem cells to replace damaged, dying, or dead brain cells. But the task isn’t easy. The brain contains thousands, if not millions, of specialized cells. Reprogramming millions of cells using the toolbox of just 20,000 or so protein-coding genes contained in the human genome seems like an impossible task.

“The math just doesn’t add up,” Mehler says. “There’s just not enough molecular diversity” in proteins to create the complexity of the brain.

“For a while, I despaired of ever being able to even think about this in my lifetime in a rational way,” Mehler says. Then he heard about noncoding RNA.

Control freaks

Some researchers estimate that as much as 98 percent of the human genome is copied into RNA, says Sofie Salama of the University of California, Santa Cruz. That figure is vastly different from what was originally postulated. Initial observations of the genome showed islands of protein-coding genes separated by vast oceans of DNA—sometimes called junk DNA—where nothing happened. That would mean that only about 2 percent of the human genome is transcribed into RNA. But recent efforts to map all of the RNA transcripts show that virtually every base pair of DNA in the human genome is copied into at least one RNA molecule, and sometimes more.

“The big question is, ‘Is this transcription meaningful?'” Salama says.

More than 20 classes of noncoding RNA have been discovered in the past decade. Many of these RNAs are much smaller than their protein-coding cousins, the messenger RNAs. Some noncoding RNAs contain a mere 20 nucleotides, the chemical units corresponding to letters in the genetic alphabet. Scientists used to throw away such short bits of RNA, thinking the tiny pieces were nothing more than breakdown products of larger molecules—basically garbage, Wahlestedt says.

Researchers now know that noncoding RNAs get involved in virtually everything that happens in or to a cell, St. Laurent says. The molecules are control freaks, touching every piece of cellular machinery. They monitor temperature, chemical conditions, electrical currents, and other signals from the environment and then tell the cell how to respond.

One class of noncoding RNAs, known as microRNAs, modulates production of proteins. MicroRNAs get their name from their minuscule size—most are only about 22 nucleotides long. These short pieces of RNA find and bind to complementary sequences in messenger RNAs. Usually that binding causes the ribosome, the protein-building machinery in a cell, to grind to a halt. The ribosome remains paused until other signals allow it to resume making protein or until the RNA message is destroyed.

Each microRNA can have multiple targets. Computer searches have predicted that a single microRNA could bind to hundreds to thousands of different messenger RNA sequences, although scientists don’t know how many of those possible targets are actually used.

“It’s not only important that you make a particular protein, but when and where you make it,” Salama says.

The brain is one place where such precise control of protein production is crucial.

Neural remodeling

Protein production at the synapses where neurons connect in the brain is vital for learning and memory, says Gerhard Schratt, a molecular neurobiologist at the University of Heidelberg in Germany, in the Nov. 2 Scientific World.

To study how connections between neurons are strengthened or weakened, Schratt and his colleagues examined the growth of spines on dendrites. Dendrites are the branchlike extensions of neurons that receive signals from other neurons. Spines look like leaf buds on the dendrite branches.

Receptors for neurotransmitters are located within the spines, which form part of the synapse. The spines are also believed to be repositories for memories, Schratt says. When incoming messages from another neuron stimulate the spine, its protein production is turned on and it grows. The total volume of the spine correlates with the strength of the synapse, Schratt says.

But just as synapses can be built and strengthened, irrelevant connections can be severed and dismantled. The connections between neurons are constantly being remodeled. And each spine on a neuron can behave independently of its neighbors, making the problem of where and when to synthesize which proteins of critical importance. Strengthen the wrong synapse and you could form a faulty memory. Sever important connections and you’ll forget something you should have remembered.

Schratt and his colleagues looked for molecules that control production in space and time in the dendritic spines. The researchers found a microRNA called miR-134 that is made only in the brain. miR-134 binds to messenger RNAs from at least four different genes and probably many others, Schratt says.

Scientists still don’t know how microRNAs find their way to the proper location in the neuron, Schratt says. He sees two possibilities: microRNAs may hitch a ride on their target messenger RNAs already heading for the spines. Or precursors of the microRNAs may contain homing signals that guide the molecules to the correct spot, bringing their target messages along, he says.

Although some of the details of how microRNAs direct protein production in spines remain fuzzy, the big picture is clear. “You need these micromanagers to be able to respond correctly,” Schratt says.

Brain power

RNA is an energy saver. Tremendous amounts of energy are required to get a protein to change its shape. RNA is more efficient. Each shape shift requires only about one-fifth of the energy it takes to force a protein into a new conformation, Mehler says.

Those energetic considerations are no small matter when you’re trying to build a better brain. If RNA wasn’t so “green,” humans would never be able to generate enough energy to power the brain. Evolution probably would have stalled at brains about the size and complexity of a mouse’s, Mehler says.

Indeed, there is some evidence that noncoding RNAs might be responsible for the emergence of the human brain.

Salama’s team was looking for regions of the human genome that had been conserved throughout most of evolution, but contained changes that separate humans from chimps and other mammalian relatives. The researchers reasoned that such DNA sequences could be genes that were once important in our ancestors, but are no longer required in humans and so have become inactive and riddled with mutations. Or, just the opposite: the sequences could be responsible for making humans human.

The researchers found 49 such sequences, called HARs for “human-accelerated regions.” About a quarter of the sequences are located next to genes known to be involved in brain development.

One sequence contained more changes than any other, making it the fastest-evolving region of the human genome. The researchers dubbed it HAR1 and discovered that the region gives rise to two different noncoding RNAs-HAR1F and HAR1R.

In a stretch of the HAR1 DNA only 118 base pairs long, the researchers found 18 differences between the human sequence and the chimp sequence. A region of that size should have only one mutation if it were evolving at the same rate as the rest of the genome. Some of the mutations altered hairpinlike structures in the RNA. Other mutations caused changes in loops of RNA that may be responsible for interacting with proteins or environmental triggers.

If HAR1 were in a protein-coding gene, it almost certainly would not have undergone as many changes, Salama says. It is very difficult to make changes without damaging a protein’s function. But RNA is more forgiving of alteration. The pool of noncoding RNA in a cell may be fodder for evolution, Salama speculates. But that doesn’t mean that RNAs can change forever without consequences.

Scientists don’t yet know how HAR1F works but do know that it is found with a protein called reelin in a group of brain cells called the Cajal-Retzius neurons. The neurons are important for establishing the six-layered structure of the cortex, the outer layer of the brain.

HAR1 may be involved in laying down the six layers of cortex properly or it could have helped expand the surface area of the cortex in humans, giving more room to think, Salama theorizes.

The last changes to HAR1 happened about 1 million years ago, she says. That means Neandertals and early human ancestors likely carried the same form of HAR1 as modern humans.

“HAR1 is probably not the thing that makes Homo sapiens Homo sapiens, but it could be important for being Homo,” Salama says.

RNA can also act as translator between the digital language of genetic material and the analog type of information contained in protein shapes, ionic concentrations, and other environmental signals, St. Laurent and Wahlestedt propose in the December Trends in Neurosciences.

Noncoding RNAs, such as the heat shock RNA, contain a sequence of bases that can pair with other bases. The pairing of bases is an on-or-off proposition, in other words, binary information. But RNA can also bend into many shapes, which can change with conditions. That gives it analog capabilities too.

The heat shock RNA changes conformation with only a 3 degree change in temperature. The shape change allows heat shock proteins to bind the RNA, setting off a cascade of reactions designed to protect the cell from heat, St. Laurent said.

For the brain to function, billions of such reactions must take place in every neuron every day. It’s a staggering engineering feat, Mehler says.

And nothing but RNA has the power, sophistication, and subtlety to perform all the tasks required for this feat, both RNA aficionados say. St. Laurent and his ilk hope the underappreciated molecule will soon get its due.

Tina Hesman Saey is the senior staff writer and reports on molecular biology. She has a Ph.D. in molecular genetics from Washington University in St. Louis and a master’s degree in science journalism from Boston University.