A research team led by scientists at Columbia’s Zuckerman Institute used techniques including single cell genomics, to describe a previously undetected RNA-mediated mechanism in mice that could explain how each sensory cell, or neuron, in mammalian noses becomes tailored to detect a specific odor chemical. “How sensory cells in the nose make their receptor choices has been one of the most vexing mysteries about olfaction,” said Stavros Lomvardas, PhD, a Herbert and Florence Irving Professor at Columbia’s Zuckerman Institute. “Now, the story behind our sense of smell, or olfaction, is becoming clearer, and also more dramatic.” Lomvardas is corresponding author of the team’s published paper in Nature, titled “RNA-mediated symmetry breaking enables singular olfactory receptor choice.”

The mammalian nose is a work of evolutionary art. Its millions of nerve cells, each tailored with just one of thousands of specific odor-chemical receptors—olfactory receptors (ORs)— encoded in the genome, can collectively distinguish a trillion distinct scents. “Olfactory receptor (OR) choice provides an extreme example of allelic competition for transcriptional dominance, where every olfactory neuron stably transcribes one of approximately 2,000 or more OR alleles,” the team explained.

For example, there are sensory neurons in our noses that bear receptors uniquely tuned to detect ethyl vanillin, the main odorant in vanilla, and other cells with receptors for limonene, lemon’s signature odorant. Those sensations, in turn, inform many behaviors, from assessing food options to discerning friends from foes to sparking memories.

The sense-refining mechanism unfolds entirely within the confines of each olfactory neuron’s nucleus. Here, each developing cell’s myriad olfactory receptor genes vie with each other in a process that winnows them down, in stages, first to handful of potentials and then to a single winner. The prevailing gene is the one that determines the cell’s odorant sensitivity. In their newly reported study, Lomvardas and his team uncovered details of the final stage of this gene selecting process.

“It’s basically a battle between a 1000 contenders,” said first author Ariel Pourmorady, an MD, PhD candidate at the Zuckerman Institute in the Lomvardas lab. The mechanism, the researchers found, is exceedingly complex at the molecular level. Gene regulatory molecules play roles that either dial up or down each gene’s ability to produce olfactory receptors. And by gathering into various alliances within the genome, these molecular players help turn specific genes on or off, to ultimately generate mature olfactory sensory neurons (mOSNs). “OR gene choice is mediated by a multichromosomal enhancer hub that activates transcription at a single OR, followed by OR-translation-dependent feedback that stabilizes this choice,” the team wrote.

The genome inside an olfactory cell’s nucleus is shown as a tangle of color-marked chromosomes with genomic locations of olfactory receptor genes revealed on the right.
The genome inside an olfactory cell’s nucleus is shown as a tangle of color-marked chromosomes with genomic locations of olfactory receptor genes revealed on the right. [Lomvardas Lab, Columbia’s Zuckerman Institute.]

Also involved is another set of molecular hubs that reshape portions of the genome in ways that favor specific receptor genes. When the team first observed these in the genome in 2014, Lomvardas dubbed them “Greek Islands” because they reminded him of islands in the Aegean Sea. “OR expression in mature OSNs (mOSNs) requires genomic interactions between the active OR allele and an intrachromosomal and interchromosomal network of 63 OR gene-specific enhancers called Greek islands (GIs),”  the team further explained.

“It turns out that the genome has a certain spatial organization in the nucleus and changes in this structure are pivotal when it comes to which genes are expressed into proteins, like olfactory receptors,” said Pourmorady. “We are learning just how important this process is within maturing olfactory cells.”

In their report in Nature the researchers summon a trove of data from mouse studies pointing to RNA as the linchpin molecule in the olfactory system’s gene-choosing mechanism. RNA is best recognized as the molecule that translates the genetic code embodied in DNA into protein molecules with specific cellular jobs, like detecting odorants.

Using sophisticated techniques for analyzing changes in genome structure as cells mature, the researchers also found new evidence pointing to a pivotal second role for the RNA. “It looks like the RNA the cell makes during gene expression also is altering the genome’s architecture in ways that bolster the expression of one olfactory receptor gene while also shutting down all the others,” Pourmorady said.

And while big gaps in this genome-controlling story remain, the researchers say the outline is becoming more defined. It starts with maturing olfactory cells, which initially express many receptor genes at those genomic hubs where gene-regulating molecules and complexes, including Greek Islands, converge. Then the RNA winnows the contending olfactory-receptor genes down to one. “… using single-cell genomics, we show formation of many competing hubs with variable enhancer composition, only one of which retains euchromatic features and transcriptional competence,” they stated.

The particular hub in each cell where the molecular stars align to produce the highest amount of RNA wins the competition. At this hub, receptor gene expression soars. However. RNA from that same hub may wind its way to all the other hubs. In those locations, the RNA causes shape changes in the genome that shut down gene expression. “… we provide evidence that OR transcription recruits enhancers and reinforces enhancer hub activity locally, whereas OR RNA inhibits transcription of competing ORs over distance, promoting transition to transcriptional singularity,” the team stated. The result is the creation of mature olfactory neurons, each of which bears on its surface only one odorant receptor.

“We are reaching the edge of science fiction when it comes to the molecular and genomic details we now can observe inside a single cell’s nucleus,” said Lomvardas. “We need to keep going back in to figure out the rest of this olfaction puzzle.” And in their paper the team concluded, “We propose that coding OR mRNAs possess non-coding functions that influence nuclear architecture, enhance their own transcription and inhibit transcription from their competitors, with generalizable implications for probabilistic cell fate decisions … Given the ever-expanding list of genes forming interchromosomal compartments in neurons, it will be interesting to investigate the non-coding role of other coding mRNAs in mutually exclusive cell fate decisions.”

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