New discovery: Synapse hiding in the mice brain may advance our understanding of neuronal communication

The latest study focused on serotonin receptors in the brain, crucial for memory, fear, and attentiveness.
Baba Tamim
3D render of super macro close-up view of neurones inside of human brain.
3D render of super macro close-up view of neurones inside of human brain.


Scientists have discovered a new type of synapse hiding in the brains of mice.

Researchers at HHMI's Janelia Research Campus in Ashburn, Virginia, have found this new kind of synapse in the tiny hairs on the surface of mice neurons, according to a press release published by the institute on Thursday.

"This special synapse represents a way to change what is being transcribed or made in the nucleus, and that changes whole programs," said David Clapham, Janelia's senior group leader.

"The effects in the cell are not just short-term – some can be long-term," added the study's lead author.

"It is like a new dock on a cell that gives express access to chromatin changes, and that is very important because chromatin changes so many aspects of the cell."

A synapse is a junction between two nerve cells that consists of a small gap through which impulses pass via neurotransmitter diffusion.

Synapses between one neuron's axon and the dendrites of other neurons are generally known to exist, but none have ever been seen between a neuron's axon (nerve fiber) and the primary cilium, microtubule-based cellular organelles that protrude from the surface of cells.

The researchers were able to peek deeply inside the cell and cilia using Janelia's high-resolution microscopes and cutting-edge equipment to study the synapse, the cell's internal signaling cascade, and alterations in the nucleus.

This discovery may advance our understanding of cell communication

New discovery: Synapse hiding in the mice brain may advance our understanding of neuronal communication
Neuron system hologram - 3d rendered image.

The identification of the ciliary synapse may advance our knowledge of how cells communicate long-term changes.

According to Clapham, the cilia, which project from the inside of the cell, close to the nucleus, to the exterior, may offer a quicker and more focused method for cells to carry out these long-term alterations.

"This was all about seeing – and Janelia enables us to see like we couldn't see before," said Clapham.

"It opens up a lot of possibilities we hadn't thought of."

It was unknown why neurons and other cells in our body continued to protrude into adulthood with this hair-like, bacterium-sized structure. Due to the fact that these cilia were challenging to see using conventional imaging methods, scientists have generally overlooked them.

However, more recent advancements in imaging technology have generated interest in these tiny extensions.

New discovery: Synapse hiding in the mice brain may advance our understanding of neuronal communication
A model of the serotonergic axo-ciliary synapse.

Game changer technique

Even though he was trained as a neurologist and neuropathologist, Shu-Hsien Sheu, a senior scientist at Janelia and the study's first author, acknowledges that he only became aware of cilia on neurons while working as a postdoc in the Clapham Lab.

Sheu was intrigued and made the decision to investigate the organelle in more detail to see what he might discover. His knowledge of focused ion beam-scanning electron microscopy, or FIB-SEM, helped him get a good gauge of the cilia.

The team was able to observe a synapse between the neuron's axon and the cilium that protruded from the cell body using the powerful microscope. The team refers to these connections as "axon-cilium" or "axo-ciliary" synapses because of their structural similarities to those of known synapses.

In order to investigate the function of this recently found structure, the scientists then created novel chemical and biosensor instruments.

Fluorescence lifetime imaging (FLIM), a newly developed imaging technique, was also used by researchers to improve assessments of the biochemical activities taking place inside the cilia.

"I learned FLIM during the pandemic to address some of the technical challenges. It turned out to be a game changer," said Sheu.

The group was able to demonstrate in detail how the neurotransmitter serotonin is delivered from the axon onto receptors on the cilia using these methods.

This starts a signaling cascade that allows modifications to the genetic material in the cell's nucleus and opens the chromatin structure.

"Function is what makes static structures come alive," said Sheu.

"Once we were confident about the structural finding, we looked deeply into its functional properties."

Sheu claims that the discovery was made possible by HHMI's curiosity-driven research philosophy, which may not have been feasible in a conventional research setting.

The latest study focused on serotonin receptors, a neurotransmitter that is widely distributed in the brain and is crucial for memory, fear, and attentiveness.

It is now necessary to look into the additional seven to ten cilia-based neurotransmitter receptors. The cilia on cells other than brain cells, such as those in the liver and kidney, merit more study.

In the future, more precise drugs may be created thanks to a greater knowledge of the function of these ciliary synapses and receptors.

The study was first published in Cell.

Study summary:

Chemical synapses between axons and dendrites mediate neuronal intercellular communication. Here, we describe a synapse between axons and primary cilia: the axo-ciliary synapse. Using enhanced focused ion beam-scanning electron microscopy on samples with optimally preserved ultrastructure, we discovered synapses between brainstem serotonergic axons and the primary cilia of hippocampal CA1 pyramidal neurons. Functionally, these cilia are enriched in a ciliary-restricted serotonin receptor, the 5-hydroxytryptamine receptor 6 (5-HTR6). Using a cilia-targeted serotonin sensor, we show that opto- and chemogenetic stimulation of serotonergic axons releases serotonin onto cilia. Ciliary 5-HTR6 stimulation activates a non-canonical Gαq/11-RhoA pathway, which modulates nuclear actin and increases histone acetylation and chromatin accessibility. Ablation of this pathway reduces chromatin accessibility in CA1 pyramidal neurons. As a signaling apparatus with proximity to the nucleus, axo-ciliary synapses short circuit neurotransmission to alter the postsynaptic neuron’s epigenetic state.

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