Engram-specific transcriptome profiling of contextual memory consolidation

Priyanka Rao-Ruiz,Michel C Van Den Oever,Steven A Kushner,Ivo M Marcelo,Rolinka J Van Der Loo,Denise E Slump,Rui M Costa,Mirjam Van Den Hout,Christian G Bouwkamp,Wilfred F Van Ijcken,Jonathan J Couey,Gabriela J Martins,Mariana R Matos

doi:10.1038/s41467-019-09960-x

Abstract

Sparse populations of neurons in the dentate gyrus (DG) of the hippocampus are causally implicated in the encoding of contextual fear memories. However, engram-specific molecular mechanisms underlying memory consolidation remain largely unknown. Here we perform unbiased RNA sequencing of DG engram neurons 24 h after contextual fear conditioning to identify transcriptome changes specific to memory consolidation. DG engram neurons exhibit a highly distinct pattern of gene expression, in which CREB-dependent transcription features prominently (P = 6.2 × 10−13), including Atf3 (P = 2.4 × 10−41), Penk (P = 1.3 × 10−15), and Kcnq3 (P = 3.1 × 10−12). Moreover, we validate the functional relevance of the RNAseq findings by establishing the causal requirement of intact CREB function specifically within the DG engram during memory consolidation, and identify a novel group of CREB target genes involved in the encoding of long-term memory.

Highlights

Sparse populations of neurons in the dentate gyrus (DG) of the hippocampus are causally implicated in the encoding of contextual fear memories
fear conditioning (FC) leads to the formation of a robust contextual fear memory (Supplementary Fig. 1b, c) with concordant dVenus expression in a sparse population of neurons distributed along the rostrocaudal axis of the DG (Supplementary Fig. 1d), consistent with prior observations of Arc expression in the DG following novel experience[12]
The number of dVenus+ cells exhibited a rapid and sustained increase following training (Fig. 1b, c). This sustained hippocampal Arc::dVenus activation was specific to the DG and not observed in the CA1 or CA3 subregions, in which dVenus+ cells were robustly observed at 5 h, but no longer at 24 h after training (Supplementary Fig. 3)

Summary

Introduction

Sparse populations of neurons in the dentate gyrus (DG) of the hippocampus are causally implicated in the encoding of contextual fear memories. We validate the functional relevance of the RNAseq findings by establishing the causal requirement of intact CREB function within the DG engram during memory consolidation, and identify a novel group of CREB target genes involved in the encoding of long-term memory. The enduring molecular dynamics necessary for memory consolidation within engram cells encoding contextual fear memories have yet to be revealed due the transient nature of most IEGs. Here, demonstrate that the IEG, Activity Regulated Cytoskeleton Associated Protein (Arc), is selectively and persistently expressed in DG engram cells after fear conditioning. Demonstrate that the IEG, Activity Regulated Cytoskeleton Associated Protein (Arc), is selectively and persistently expressed in DG engram cells after fear conditioning This sustained expression of Arc enabled us to examine the differential transcriptional profile of DG memory-trace neurons compared to their nonactivated neighbors, 24 h after fear conditioning. Unbiased upstream analysis revealed the CREB network to be activated exclusively in engram neurons after fear conditioning (FC), a finding causally validated by manipulating CREB function in engram neurons

Methods

Results

Conclusion