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Transcriptome and epigenome analysis of engram cells: Next-generation sequencing technologies in memory research

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The central importance of nuclear mechanisms in the storage of memory

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Separate orexigenic hippocampal ensembles shape dietary choice by enhancing contextual memory and motivation

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Synaptically-targeted long non-coding RNA SLAMR promotes structural plasticity by increasing translation and CaMKII activity

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Neuronal enhancers fine-tune adaptive circuit plasticity

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Cell type–specific epigenetic priming of gene expression in nucleus accumbens by cocaine

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Epigenetic Mechanisms of Brain Sexual DifferentiationPreprint

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SATB2 organizes the 3D genome architecture of cognition in cortical neurons

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MIAOME: Human microbiome affect the host epigenome

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Neuromorphic Optical Data Storage Enabled by Nanophotonics: A Perspective

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The dynamics of chromatin architecture in brain development and function

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An unbiased AAV-STARR-seq screen revealing the enhancer activity map of genomic regions in the mouse brain in vivo

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Activation-induced chromatin reorganization in neurons depends on HDAC1 activity

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Epigenetic and Transcriptional Regulation of Spontaneous and Sensory Activity Dependent Programs During Neuronal Circuit Development

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Targeting mitochondrial dynamics of morphine-responsive dopaminergic neurons ameliorates opiate withdrawal

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Epigenetic Changes and Chromatin Reorganization in Brain Function: Lessons from Fear Memory Ensemble and Alzheimer’s Disease

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Decoding brain memory formation by single-cell RNA sequencing

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Remembering through the genome: the role of chromatin states in brain functions and diseases

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Aging differentially alters the transcriptome and landscape of chromatin accessibility in the male and female mouse hippocampus

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Cell type-specific chromatin accessibility analysis in the mouse and human brain

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Comprehensive Analysis of Mouse Hippocampal Lysine Acetylome Mediated by Sea Cucumber Peptides Preventing Memory Impairment

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Transcription and epigenetic factor dynamics in neuronal activity-dependent gene regulation

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CBP Is Required for Establishing Adaptive Gene Programs in the Adult Mouse Brain

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From cellular to fear memory: An epigenetic toolbox to remember

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Histone macroH2A1 is a stronger regulator of hippocampal transcription and memory than macroH2A2 in mice

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Stress and the brain transcriptome: Identifying commonalities and clusters in standardized data from published experiments

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Three-dimensional chromatin organization in brain function and dysfunction

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Cell-type specific profiling of histone post-translational modifications in the adult mouse striatum

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The epigenome under pressure: On regulatory adaptation to chronic stress in the brain

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Early-life stress and ovarian hormones alter transcriptional regulation in the nucleus accumbens resulting in sex-specific responses to cocaine

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Cell-type- and locus-specific epigenetic editing of memory expression

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Altered Activity-Regulated H3K9 Acetylation at TGF-Beta Signaling Genes During Egocentric Memory in Huntington's Disease

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Characterization of transcriptional profiles associated with stress-induced neuronal activation in Arc-GFP mice

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All IEGs Are Not Created Equal—Molecular Sorting Within the Memory Engram

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Hippocampal cells multiplex positive and negative engramsPreprint

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Astroengrams: rethinking the cellular substrate for memory

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Rapid nucleus-scale reorganization of chromatin in neurons enables transcriptional adaptation for memory consolidation

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Epigenetics in Learning and Memory

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The molecular and cellular basis of memory engrams: Mechanisms of synaptic and systems consolidation

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Mutant FUS induces chromatin reorganization in the hippocampus and alters memory processes

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Unveiling Transcriptional and Epigenetic Mechanisms Within Engram Cells: Insights into Memory Formation and Stability

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The molecular diversity of plasticity mechanisms underlying memory: An evolutionary perspective

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Hippocampal DNA Methylation Promotes Contextual Fear Memory Persistence by Facilitating Systems Consolidation and Cortical Engram Stabilization

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Chromatin Remodeling Factor SMARCA5 is Essential for Hippocampal Memory Maintenance via Metabolic Pathways in Mice

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Serotonin signaling at cilia synapses

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Activity-dependent remodeling of genome architecture in engram cells facilitates memory formation and recall

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Differential Activation States of Direct Pathway Striatal Output Neurons during l-DOPA-Induced Dyskinesia Development

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3D Genome Plasticity in Normal and Diseased Neurodevelopment

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DNA repair enzyme NEIL3 enables a stable neural representation of space by shaping transcription in hippocampal neurons

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Thalamocortical transcriptional gates coordinate memory stabilization

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Altered morphological characteristics and structural covariance connectivity associated with verbal working memory performance in ADHD children

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Molecular and cellular mechanisms of engram allocation and maintenance

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The elusive transcriptional memory trace

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Kdm4a is an activity downregulated barrier to generate engrams for memory separation

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Brain Metabolic DNA: A Long Story and Some Conclusions

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Hippocampal Cannabinoid 1 Receptors Are Modulated Following Cocaine Self-administration in Male Rats

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Can 3D diploid genome reconstruction from unphased Hi-C data be salvaged?

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Spatially resolved transcriptomic signatures of hippocampal subregions and Arc-expressing ensembles in active place avoidance memory

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Integrating physiological and transcriptomic analyses at the single-neuron level

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Activity-dependent transcriptional programs in memory regulate motor recovery after stroke

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Molecular and developmental deficits in Smith-Magenis syndrome human stem cell-derived cortical neural models

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Single-cell resolution spatial transcriptomic signature of the retrosplenial cortex during memory consolidation

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Spatial transcriptomic profiling uncovers the molecular effects of the neurotoxicant polychlorinated biphenyls (PCBs) in the brains of adult mice

Basu, B., Breese, N. M., Lombardi, S., Wang, H. M., Li, X., Tiburcio, D., Niemasz, Z., Beyer, S. E., Dean, L. E., Marek, R. F., et al. (2026) · Molecular Psychiatry · doi:10.1038/s41380-026-03466-x · Cited by 3 · see citing works

Oxytocin attenuates the retrieval of methamphetamine-associated reward memories by enhancing adult hippocampal neurogenesis in mice

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Altered postnatal chromatin development in the nucleus accumbens primes lifelong stress sensitivityPreprint

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Learning induces persistent chromatin loops underlying robust gene expression during memory recallPreprint

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Genetic Mechanisms of Experience-Dependent Neuronal Plasticity

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Extended fear learning enhances excitatory and inhibitory synaptic transmission onto amygdala engram cells

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Memory engram synapse 3D macromolecular architecture visualized by cryoCLEM-guided cryoET

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Forgetting Is Not the Mere Opposite of Learning

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Memory Storage in Distributed Engram Cell Ensembles

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Time-Dependent Transcriptional Dynamics of Contextual Fear Memory Retrieval Reveals the Function of Dipeptidyl Peptidase 9 in Reconsolidation

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DNA Methylation in Long-Term Memory

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Genome-wide chromatin recording resolves dynamic cell state changes

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Persistent open chromatin state in early-life stress-activated cells of the VTA

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Statistical curve models for inferring 3D chromatin architecture

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Dynamics of transcriptional programs and chromatin accessibility in mouse spermatogonial cells from early postnatal to adult lifePreprint

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Lysine crotonylation acts as an epigenetic switch for glutamate neurotransmission and spatial memory

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Programmed DNA breaks drive chromatin reconfiguration and facilitate transcriptional potentiation at neuronal early response genesPreprint

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Activity-dependent remodeling of genome architecture in engram cells facilitates memory formation and recall

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Memory encoding reprograms neuronal transcriptional responses via durable chromatin remodelingPreprint

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Brain-wide Epigenetic Mapping of Memory Engram Cells

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Unveiling Transcriptional and Epigenetic Mechanisms Within Engram Cells: Insights into Memory Formation and Stability

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Transcriptome and epigenome analysis of engram cells: Next-generation sequencing technologies in memory research

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