Spatiotemporal multi-omics analysis reveals distinct epigenetic and transcriptional signatures in the hippocampal-amygdala circuit during fear memory consolidation

The consolidation of contextual fear memories requires the crosstalk among multiple brain regions, including the hippocampus and amygdala. Despite the advance in single cell transcriptomic techniques, tracing the dynamic gene expression across the hippocampal-amygdala circuit remain challenging. Here we integrated high resolution spatial transcriptomics with single nuclei multi-omics techniques to systematically investigate the spatiotemporally transcriptional programs across the hippocampal-amygdala circuit during the encoding and retrieval of contextual fear memory. It reveals highly dynamic gene expression in the subregions of hippocampus and amygdala. Our data provide new insights into the transcriptional programs underlying consolidation of memory. Overall design: Adult C57BL/6 male mice (12~15 weeks) were subjected to contextual fear conditioning (CFC), mice without foot shock were used as context control (CC), and mice stayed in the home cage until sample harvest were used as home cage control (HC). Mice were harvested 1h or 4h after foot shock on the training day (day 0) and 4h after memory retrieval on day 1 to assess fear memory consolidation and reconsolidation. To profile spatial transcriptome, the mouse brains were freshly isolated to prepare FFPE tissue blocks, then coronally sectioned and placed onto the Visium slides for Visium Spatial Gene Expression library preparation. To simultaneously profile the transcriptome and chromatin accessibility at single cell resolution, hippocampus and amygdala were micro-dissected from the freshly isolated mouse brain tissues for single nuclei suspension preparation and subsequently loaded onto the Chromium iX using the single nucleus multiome kit from 10x genomics. Single nucleus RNA-seq (snRNA-seq) and single nucleus ATAC-seq (snATAC-seq) libraries were simultaneously constructed from the same nucleus following the manufactures' instructions.