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“Morpheus: If you're talking about what you can feel, what you can smell, what you can taste and see, then real is simply electrical signals interpreted by your brain.”
-The Matrix, Warner Bros., 1999

A truth that helped make the science fiction of The Matrix compelling is that the conscious mind does not directly perceive the world, but instead depends on the reports of sensory neurons to know what is going on around it. In The Matrix computer programs manipulate sensory neurons electronically. In recent research produced by a group led by Patrik Ernfors based at the Karolinska Institute, the sensory neurons are manipulated by microRNAs.

Misfiring Nerves

These findings are important because the biochemical changes described can contribute to the sensation of chronic pain, which can be debilitating. Pain receptors are sensory neurons that normally respond to tissue-damaging heat, pressure, and chemicals. These responses are obviously important to survival, motivating us to move away from dangerous situations. When chronic pain develops as a result of nerve damage, these receptors are more easily triggered to fire, and they can fire despite the lack of tissue-damaging stimuli. In addition, light-touch receptors can be inappropriately recruited into reporting pain sensations. That is, the signals that normally indicate gentle touches are redirected as pain signals.

MicroRNA biogenesis. Based on Wienholds and Plasterk, FEBS Letters 2005, 579: 5911-5922. (Exiqon)

MicroRNA biogenesis. Based on Wienholds and Plasterk, FEBS Letters 2005, 579: 5911-5922. (Exiqon)

Genome Doesn’t Make Junk

Our knowledge of the importance of microRNAs has steadily increased this century. They are not something that the founders of molecular biology could have envisioned. The genome is the collection of genes and DNA any organism has. In 1958 Francis Crick put forward the “Central Dogma of Molecular Biology” which states that genetic information in a cell is transferred from the DNA genome to RNA (which is very similar to DNA) to protein. The understanding was that proteins carried out the vast majority of activities of life, while DNA, with the help of RNA, provided the information to make proteins.

This theory worked extremely well, but there were two strange paradoxes that were noted over time. The first paradox is although bacteria use about 85% of their DNA genome to make proteins, humans use less than 2%. If the job of the human DNA genome is merely to make protein, 98% is not directly involved in this work. All this extra DNA not making protein was referred to as “junk DNA.”

Another problem was the observation that a typical bacteria gets by with 4,000 protein-coding genes. Given our complexity, it was thought that humans must have something like 500,000. However, when the human genome was sequenced, only about 23,000 protein-coding genes could be identified.

We can start to make sense of these two contrary findings if human genes are more complex than bacterial genes (they are) and if noncoding DNA actually has a functional role (much of it does). MicroRNAs come from DNA that doesn’t make protein and helps regulate complex genes that do. They are very short, about 10% of the length of a typical RNA. When microRNAs recognize a protein-coding RNA they can reduce its translation into protein. This adds another layer of complexity to the regulation of protein-coding genes.

Powerful Experimental Design

The ultimate test of the function of a gene is to see what happens in a living system when it is eliminated. The Ernfors group designed a way to eliminate a specific cluster of microRNAs, microRNA-183, in specific neurons in mice. They took advantage of the Cre-LoxP system. In certain viruses an enzyme, Cre, cuts out DNA between two copies of a sequence called LoxP as part of its normal life cycle. It then repairs the remaining DNA. Scientists can insert the LoxP sequence around their favorite gene in mice. When the gene is flanked by LoxP: it is “floxed.” They may have a second strain of mice in which the Cre gene is under the control of sequences which will drive its RNA and protein production in specific cells. When they mate these two strains of mice, the resulting mice pups will contain cells that produce Cre and lose the floxed gene. The cells that don’t produce Cre don’t lose the gene.

By Matthias Zepper (Curnen).

By Matthias Zepper (Curnen). (CC BY-SA 3.0)

Using this strategy, the Ernfors group was able to create three kinds of mice: one that lacks microRNA-183 gene in all sensory nerves, a second that lacks the gene in their light-touch receptors, and a third that lacks the gene in their pain receptors.

Sensitive to Touch

Mice that lacked microRNA-183 in all sensory neurons, and those that lacked it only in their pain receptors, were especially sensitive to touch. These mice showed sensitivity even when running on their wheel, although this is usually painless. This kind of stimulation is a step above light touch, and the light-touch neurons weren’t implicated in this response. The Ernfors group was able to show that 33 protein-coding genes had altered expression patterns in neurons from these mice.

Two genes that made increased RNA (and one would assume protein) were calcium channel proteins. Channel proteins let positive or negative ions in and out of the cells through a channel in the membrane. All cells move ions in and out of themselves to produce a net negative charge. Nerve cells are remarkable because they can temporarily depolarize to a positive charge when stimulated. The extra calcium channel proteins in these nerve cells brought on by the lack of microRNA-183 seems to make them more easily stimulated. Drugs that are effective against chronic pain reversed these effects.

Wires Crossed

Mice and people with nerve injury can develop chronic pain. In mice with nerve injury, there was reduced expression of microRNA-183 in all sensory neurons. Mice that lacked the microRNA-183 gene in their soft touch receptors were especially sensitive after nerve injury in this experiment. It appears that nerves that usually report soft touch were instead reporting pain.

Shining Light on the Pain Problem

To further illuminate the mechanism by which chronic pain develops the Ernfors group produced mice that carried the Channelrhodopsin gene. This gene allows for the influx of ions into a neuron (and therefore its activation) when the neuron has light shone on it by an optical fiber in a technique called “optogenetics.” The optical fiber can be precisely located so that only one cell, or cell type, is activated.

When soft-touch receptors were activated by optogenetics they showed increased mechanical sensitivity but no signs of pain. However, mice with nerve injury and optogenetically stimulated soft-touch receptors did show signs of pain. A calcium channel protein was expressed in these nerves, and microRNA-183 suppressed the expression of calcium channel proteins in this experiment. It seems that microRNA-183 loss can’t turn a soft touch receptor into a pain receptor, but the presence of this microRNA limits the efficiency with which a soft touch receptor is turned into a pain receptor.

A World Where Anything Is Possible

The research by Patrik Ernfors group supports the idea that microRNA-183 consistently acts against the development of chronic pain. This suggests that this debilitating condition may be alleviated by finding ways to boost it the expression of this microRNA. Alternatively, there are a group of genes up-regulated and down-regulated as a result of microRNA-183 expression. Each one of these protein products may be a candidate as a drug target. If these experimental programs are successful we may, like the heroes of The Matrix, master our perception of pain.

Top image: A person showing feeling of pain. (CC BY-ND 2.0)


Cassels, L. & Barde, Y.-A., 2017. Scailing pain threashold with microRNAs. Science, 356(6343), pp. 1124-1125.

Exiqon, What are microRNAs?. [Online]
Available at:
[Accessed 8 July 2017].

PENG, C. et al. 2017. miR-183 cluster scales mechanical pain sensitivity by regulating basal and neuropathic pain genes. Science, 356(6343), pp. 1168-1171.

James Murphy's picture

James Murphy

James had his first exposure to laboratory research as a twenty-year old when he began working as a technician at the Columbia University Comprehensive Cancer Center. He eventually earned his doctorate in Biochemistry from New York University. His training focused on cancer biology and gene expression. Specifically he looked at mutation in cancer cells using the then relatively new Polymerase Chain Reaction technique that allows one to mass-produce copies of a DNA sample from small amounts of s...Read More

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