Neuronal types in the mouse amygdala and their transcriptional response to fear conditioning

Hannah Hochgerner, Shelly Singh, Muhammad Tibi, Zhige Lin, Niv Skarbianskis, Inbal Admati, Osnat Ophir, Nuphar Reinhardt, Shai Netser, Shlomo Wagner, Amit Zeisel

Research output: Contribution to journalArticlepeer-review


The amygdala is a brain region primarily associated with emotional response. The use of genetic markers and single-cell transcriptomics can provide insights into behavior-associated cell state changes. Here we present a detailed cell-type taxonomy of the adult mouse amygdala during fear learning and memory consolidation. We perform single-cell RNA sequencing on naïve and fear-conditioned mice, identify 130 neuronal cell types and validate their spatial distributions. A subset of all neuronal types is transcriptionally responsive to fear learning and memory retrieval. The activated engram cells upregulate activity-response genes and coordinate the expression of genes associated with neurite outgrowth, synaptic signaling, plasticity and development. We identify known and previously undescribed candidate genes responsive to fear learning. Our molecular atlas may be used to generate hypotheses to unveil the neuron types and neural circuits regulating the emotional component of learning and memory.

Original languageEnglish
Pages (from-to)2237-2249
Number of pages13
JournalNature Neuroscience
Issue number12
StatePublished - Dec 2023

Bibliographical note

Publisher Copyright:
© 2023, The Author(s).


  • Amygdala/physiology
  • Animals
  • Fear/physiology
  • Memory/physiology
  • Mice
  • Neuronal Plasticity/genetics
  • Neurons/physiology


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