Distinct transcriptomic profiles in the dorsal hippocampus and prelimbic cortex are transiently regulated following episodic learning

Aaron Katzman, Alireza Khodadadi-Jamayran, Dana Kapeller-Libermann, Xiaojing Ye, Aristotelis Tsirigos, Adriana Heguy, Cristina M. Alberini

Research output: Contribution to journalArticlepeer-review


A fundamental, evolutionarily conserved biological mechanism required for long-term memory formation is rapid induction of gene transcription upon learning in relevant brain areas. For episodic types of memories, two regions undergoing this transcription are the dorsal hippocampus (dHC) and prelimbic (PL) cortex. Whether and to what extent these regions regulate similar or distinct transcriptomic profiles upon learning remain to be understood. Here, we used RNA sequencing in the dHC and PL cortex of male rats to profile their transcriptomes in untrained conditions (baseline) and at 1 h and 6 d after inhibitory avoidance learning. We found that, of 33, 713 transcripts, .14, 000 were significantly expressed at baseline in both regions and ;3000 were selectively enriched in each region. Gene Ontology biological pathway analyses indicated that commonly expressed pathways included synapse organization, regulation of membrane potential, and vesicle localization. The enriched pathways in the dHC were gliogenesis, axon development, and lipid modification, while in the PL cortex included vesicle localization and synaptic vesicle cycle. At 1 h after learning, 135 transcripts changed significantly in the dHC and 478 in the PL cortex; of these, only 34 were shared. Biological pathways most significantly regulated by learning in the dHC were protein dephosphorylation, glycogen and glucan metabolism, while in the PL cortex were axon development and axonogenesis. The transcriptome profiles returned to baseline by 6 d after training. Thus, a significant portion of dHC and PL cortex transcriptomic profiles is divergent, and their regulation upon learning is largely distinct and transient.

Original languageEnglish (US)
Pages (from-to)2601-2614
Number of pages14
JournalJournal of Neuroscience
Issue number12
StatePublished - Mar 24 2021


  • Hippocampus
  • Memory
  • Prelimbic cortex
  • RNAseq
  • Transcriptomic
  • Hippocampus/physiology
  • Rats, Long-Evans
  • Memory, Episodic
  • Rats
  • Male
  • Transcriptome/physiology
  • Fear/physiology
  • Gene Regulatory Networks/physiology
  • Animals
  • Avoidance Learning/physiology
  • Prefrontal Cortex/physiology

ASJC Scopus subject areas

  • General Neuroscience


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