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Advances in the labelling and selective manipulation of synapses

Nature Reviews Neuroscience volume 25, pages 668–687 (2024)Cite this article

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Abstract

Synapses are highly specialized neuronal structures that are essential for neurotransmission, and they are dynamically regulated throughout the lifetime. Although accumulating evidence indicates that these structures are crucial for information processing and storage in the brain, their precise roles beyond neurotransmission are yet to be fully appreciated. Genetically encoded fluorescent tools have deepened our understanding of synaptic structure and function, but developing an ideal methodology to selectively visualize, label and manipulate synapses remains challenging. Here, we provide an overview of currently available synapse labelling techniques and describe their extension to enable synapse manipulation. We categorize these approaches on the basis of their conceptual bases and target molecules, compare their advantages and limitations and propose potential modifications to improve their effectiveness. These methods have broad utility, particularly for investigating mechanisms of synaptic function and synaptopathy.

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Fig. 1: Strategies to label synaptically connected neurons.
Fig. 2: Strategies to label synaptic proteins.
Fig. 3: GRASP-based techniques to label synaptic interactions.
Fig. 4: Further techniques for labelling interactions between presynaptic and postsynaptic compartments.
Fig. 5: Synapse manipulation techniques.

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Acknowledgements

This work was supported by a grant from the Institute of Basic Science (IBS-R001-E1-2023-a00). Figures were created with BioRender.com.

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  1. Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, South Korea

    Binod Timalsina, Sangkyu Lee & Bong-Kiun Kaang

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  1. Binod Timalsina
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  2. Sangkyu Lee
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Glossary

Active zone

The part of the presynaptic membrane that is the major site for the fusion of synaptic vesicles and neurotransmitter release.

Anterograde tracing

A method used to trace axonal projections from the cell body to the axon terminals.

Binary expression system

A transgene expression system that is based on a single exogenous DNA-binding protein (driver) binding to a unique recognition motif (responder). For example, LexA protein recognizes the LexA operator, whereas QF DNA-binding protein acts on QUAS sequence.

CRISPR–Cas9

A genome editing tool that acts as ‘molecular scissors’ by using CRISPR sequences as a guide to recognize and cut DNA at a specific location, enabling the manipulation of genetic DNA.

Engram cells

Neurons that are activated during memory formation and are believed to be the neuronal substrate of memory storage.

Engram synapses

Activated synapses between pairs of engram cells that serve as a marker of memory formation.

Fusion proteins

Proteins derived by combining two or more distinct protein domains that are encoded by separate genes but are transcribed and translated as a single polypeptide chain.

Gal4 driver line

A transgenic line of fruitflies expressing the Gal4 transcription factor in specific cell populations or at specific times. Gal4 can activate the expression of target genes under the control of upstream activating sequence elements.

Genome editing

A genetic engineering method in which the DNA of an organism or a cell is manipulated via the insertion, deletion or replacement of sequences in the genome.

Guide RNAs

Specific RNA sequences that recognize the regions of interest within DNA and act as a guide for the Cas proteins that target precise DNA editing.

Homology-directed repair

(HDR). A mechanism to repair a double-strand DNA break in cells by using a homologous sequence of sister chromatids as a repair template.

Immediate early genes

(IEGs). Genes that are activated rapidly and transiently upon the neuronal activation in response to various cellular stimuli.

Intrabodies

Antibodies targeting the endogenous proteins that interact within a cell.

Non-homologous end-joining

(NHEJ). The predominant pathway for the repair of double-strand breaks in DNA, regardless of the sequence homology.

Optogenetic actuators

Light-sensitive proteins that can control specific molecular or cellular activity.

Reactive oxygen species

A type of highly reactive molecules and free radicals derived from molecular oxygen with one or more unpaired electrons in the outer orbital. ROS serves as signalling molecules in normal biological processes.

Recombinases

Enzymes that catalyse site-specific DNA recombination events, which allow the exchange of DNA fragments.

Retrograde tracing

The process by which neuronal processes are traced from the axon terminals towards the cell body.

Synaptopathy

Dysfunction of the nervous system (including the brain, spinal cord and peripheral nervous system) that is related to altered synapse formation and function.

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Timalsina, B., Lee, S. & Kaang, BK. Advances in the labelling and selective manipulation of synapses. Nat. Rev. Neurosci. 25, 668–687 (2024). https://doi.org/10.1038/s41583-024-00851-9

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