Learning and Memory

Visualization of neuronal network activity and plasticity 

During learning and memory formation, gene expression is dynamically regulated in response to experience-dependent neuronal activity. In particular, the expression of immediate-early genes (IEGs) including c-fos, and Arc is rapidly and transiently altered in specific neurons or neuronal ensembles in brain areas involved in the learning and memory processing of a certain task/activity. Therefore, the visualization of IEG mRNA expression patterns have widely been used as a molecular readout for neuronal populations that are engaged in generating and encoding long-term memories. 

To further characterize activated neuronal cell populations, RNAscope multiplexing capability enables IEG mRNA detection in combination with other targets or cell type markers. 

Here, we detect neuronal activity in the mouse brain hippocampus by using the RNAscope assay to visualize Cfos which is a proto-oncogene and transcription factor that is induced within 15 minutes of stimulation (Figure 1). Simultaneously, we used a second probe to detect Chrm3-positive neurons.

FIGURE 1. Detection of the transcription factor immediate early gene and activity marker Cfos (Green) in combination with the G protein-coupled receptor Cholinergic Receptor Muscarinic 3 (Chrm3, Red) in normal mouse brain hippocampus using the RNAscope™ Multiplex Fluorescent assay on Fresh Frozen tissue samples. Cells are counterstained with DAPI. CA = Cornu Ammonis.

To detect neuronal plasticity, the expression of the effector immediate early gene Activity-Regulated Cytoskeleton-associated protein Arc (also known as Arg3.1) is visualized in Figure 2 in combination with a probe targeted to Drd1.

FIGURE 2. (Right panel) Detection of the effector immediate early gene and plasticity marker Arc (Green) in combination with the G protein-coupled Dopamine Receptor D1 (Drd1, Red) in normal mouse brain striatum using the RNAscope Multiplex Fluorescent assay on Fresh Frozen tissue samples. (Top left panel) Single-channel image for Drd1 (Red). (Bottom left panel) Single-channel image for Arc (Green).


  • Guzowski JF. Insights into immediate-early gene function in hippocampal memory consolidation using antisense oligonucleotide and fluorescent imaging approaches. Hippocampus 2002; 12:86-104

Application Note

Learn more in our RNAscope Neuroscience Application Note - Detection of RNA in the central and peripheral nervous system using the RNAscope in situ hybridization assay

Detection of RNA in the central and peripheral nervous system using the RNAscope in situ hybridization assay

Fill out the form below to download the application note:

Neuroscience Gene List

(click on gene name to access corresponding RNAscope probes)




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