Uncovering memory-related gene expression in contextual fear conditioning using ribosome profiling.

Konstanze Simbriger,Inês S Amorim,Stella Kouloulia,Gilliard Lach,Seyed Mehdi Jafarnejad,Kleanthi Chalkiadaki,Christos G Gkogkas,Arkady Khoutorsky

doi:10.1016/j.pneurobio.2020.101903

Konstanze Simbriger, Inês S Amorim + Show 6 more

Open Access

https://doi.org/10.1016/j.pneurobio.2020.101903

Copy DOI

Abstract

Contextual fear conditioning (CFC) in rodents is the most widely used behavioural paradigm in neuroscience research to elucidate the neurobiological mechanisms underlying learning and memory. It is based on the pairing of an aversive unconditioned stimulus (US; e.g. mild footshock) with a neutral conditioned stimulus (CS; e.g. context of the test chamber) in order to acquire associative long-term memory (LTM), which persists for days and even months. Using genome-wide analysis, several studies have generated lists of genes modulated in response to CFC in an attempt to identify the “memory genes”, which orchestrate memory formation. Yet, most studies use naïve animals as a baseline for assessing gene-expression changes, while only few studies have examined the effect of the US alone, without pairing to context, using genome-wide analysis of gene-expression. Herein, using the ribosome profiling methodology, we show that in male mice an immediate shock, which does not lead to LTM formation, elicits pervasive translational and transcriptional changes in the expression of Immediate Early Genes (IEGs) in dorsal hippocampus (such as Fos and Arc), a fact which has been disregarded by the majority of CFC studies. By removing the effect of the immediate shock, we identify and validate a new set of genes, which are translationally and transcriptionally responsive to the association of context-to-footshock in CFC, and thus constitute salient “memory genes”.

Highlights

Contextual fear conditioning (CFC) in rodents is the most widely used behavioural paradigm in l neuroscience research to elucidate the neurobiological mechanisms underlying learning and memory. a It is based on the pairing of an aversive unconditioned stimulus (US; e.g. mild footshock) with a neutral n conditioned stimulus (CS; e.g. context of the test chamber) in order to acquire associative long-term r memory (LTM), which persists for days and even months
Using the ribosome profiling methodology, we show that in male mice an immediate shock, which does not lead to LTM formation, elicits pervasive translational and transcriptional changes in the expression of Immediate Early Genes (IEGs) in dorsal hippocampus, a fact which has been disregarded by the majority of CFC studies
To further elucidate the mechanisms linked to mRNA untranslated region (UTR), which are implicated in contextual memory acquisition, we employed UTRscan and the database of UTR motifs UTRdb[15] and analysed the 5 or 3 UTR sequences of CFC and immediate shock DTGs and detected several known motifs implicated in translational control (Fig 3b)

Summary

Introduction

Using the ribosome profiling methodology, we show that in male mice an immediate shock, which does not lead to LTM formation, elicits pervasive translational and transcriptional changes in the expression of Immediate Early Genes (IEGs) in dorsal hippocampus (such as Fos and Arc), a fact which has been disregarded by the majority of CFC studies. CFC and immediate shock engendered pervasive translational and transcriptional changes in dorsal hippocampus 20 min after terminating the respective protocol, as compared to homecage group animals (Fig. 1c, d).

Results

Conclusion