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

Molecular and cellular mechanisms of engram allocation and maintenance

(2021) Kubra Gulmez Karaca et al.   BRAIN RESEARCH BULLETIN

Memory engrams: Recalling the past and imagining the future

(2020) Sheena A. Josselyn et al.   SCIENCE

Locus-specific DNA methylation of Mecp2 promoter leads to autism-like phenotypes in mice

(2020) Zongyang Lu et al.   Cell Death & Disease

Neuronal ensemble-specific DNA methylation strengthens engram stability

(2020) Kubra Gulmez Karaca et al.   Nature Communications

Nr4a1 suppresses cocaine-induced behavior via epigenetic regulation of homeostatic target genes

(2020) Marco D. Carpenter et al.   Nature Communications

Functionally Distinct Neuronal Ensembles within the Memory Engram

(2020) Xiaochen Sun et al.   CELL

CRISPR/Cas Derivatives as Novel Gene Modulating Tools: Possibilities and In Vivo Applications

(2020) Xingbo Xu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

KAT3-dependent acetylation of cell type-specific genes maintains neuronal identity in the adult mouse brain

(2020) Michal Lipinski et al.   Nature Communications

A Sparse, Spatially Biased Subtype of Mature Granule Cell Dominates Recruitment in Hippocampal-Associated Behaviors

(2020) Sarah R. Erwin et al.   Cell Reports

In vivo locus-specific editing of the neuroepigenome

(2020) Yun Young Yim et al.   NATURE REVIEWS NEUROSCIENCE

An Activity-Mediated Transition in Transcription in Early Postnatal Neurons

(2020) Hume Stroud et al.   NEURON

Epigenomically Bistable Regions across Neuron-Specific Genes Govern Neuron Eligibility to a Coding Ensemble in the Hippocampus

(2020) Shannon C. Odell et al.   Cell Reports

Mapping the epigenomic and transcriptomic interplay during memory formation and recall in the hippocampal engram ensemble

(2020) Asaf Marco et al.   NATURE NEUROSCIENCE

The role of neuronal excitability, allocation to an engram and memory linking in the behavioral generation of a false memory in mice

(2020) Jocelyn M.H. Lau et al.   NEUROBIOLOGY OF LEARNING AND MEMORY

Dynamic and heterogeneous neural ensembles contribute to a memory engram

(2020) Brian M Sweis et al.   CURRENT OPINION IN NEUROBIOLOGY

Temporal evolution of cortical ensembles promoting remote memory retrieval

(2019) Laura A. DeNardo et al.   NATURE NEUROSCIENCE

Enhancer Histone Acetylation Modulates Transcriptional Bursting Dynamics of Neuronal Activity-Inducible Genes

(2019) Liang-Fu Chen et al.   Cell Reports

How the epigenome integrates information and reshapes the synapse

(2019) Rianne R. Campbell et al.   NATURE REVIEWS NEUROSCIENCE

Distinct hippocampal engrams control extinction and relapse of fear memory

(2019) Anthony F. Lacagnina et al.   NATURE NEUROSCIENCE

Memory formation in the absence of experience

(2019) Gisella Vetere et al.   NATURE NEUROSCIENCE

LADL: light-activated dynamic looping for endogenous gene expression control

(2019) Ji Hun Kim et al.   NATURE METHODS

Engram-specific transcriptome profiling of contextual memory consolidation

(2019) Priyanka Rao-Ruiz et al.   Nature Communications

CUT&Tag for efficient epigenomic profiling of small samples and single cells

(2019) Hatice S. Kaya-Okur et al.   Nature Communications

Immediate and deferred epigenomic signatures of in vivo neuronal activation in mouse hippocampus

(2019) Jordi Fernandez-Albert et al.   NATURE NEUROSCIENCE

Single-cell memory trace imaging with immediate-early genes

(2019) Magdalena Sauvage et al.   JOURNAL OF NEUROSCIENCE METHODS

Capturing activated neurons and synapses

(2019) Jung-Eun Choi et al.   NEUROSCIENCE RESEARCH

Memory Allocation: Mechanisms and Function

(2018) Sheena A. Josselyn et al.   Annual Review of Neuroscience

Rescue of Fragile X Syndrome Neurons by DNA Methylation Editing of the FMR1 Gene

(2018) X. Shawn Liu et al.   CELL

dCas9: A Versatile Tool for Epigenome Editing

(2018) Daan J.W. Brocken et al.   CURRENT ISSUES IN MOLECULAR BIOLOGY

A CRISPR–dCas Toolbox for Genetic Engineering and Synthetic Biology

(2018) Xiaoshu Xu et al.   JOURNAL OF MOLECULAR BIOLOGY

Author Correction: CRISPR interference-based specific and efficient gene inactivation in the brain

(2018) Yi Zheng et al.   NATURE NEUROSCIENCE

The role of engram cells in the systems consolidation of memory

(2018) Susumu Tonegawa et al.   NATURE REVIEWS NEUROSCIENCE

Epigenome Interactions with Patterned Neuronal Activity

(2018) Jillian Belgrad et al.   NEUROSCIENTIST

Interregional synaptic maps among engram cells underlie memory formation

(2018) Jun-Hyeok Choi et al.   SCIENCE

Single-Cell Multi-omics: An Engine for New Quantitative Models of Gene Regulation

(2018) Jonathan Packer et al.   TRENDS IN GENETICS

The hippocampal engram maps experience but not place

(2018) Kazumasa Z. Tanaka et al.   SCIENCE

Epigenetic regulation of the circadian gene Per1 contributes to age-related changes in hippocampal memory

(2018) Janine L. Kwapis et al.   Nature Communications

A novel environment-evoked transcriptional signature predicts reactivity in single dentate granule neurons

(2018) Baptiste N. Jaeger et al.   Nature Communications

Activity-Regulated Transcription: Bridging the Gap between Neural Activity and Behavior

(2018) Ee-Lynn Yap et al.   NEURON

Molecular Mechanisms of the Memory Trace

(2018) Arun Asok et al.   TRENDS IN NEUROSCIENCES

Bridging Synaptic and Epigenetic Maintenance Mechanisms of the Engram

(2018) Madeleine Kyrke-Smith et al.   Frontiers in Molecular Neuroscience

Heroes of the Engram

(2017) Sheena A. Josselyn et al.   JOURNAL OF NEUROSCIENCE

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

(2017) Ilya M. Flyamer et al.   NATURE

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

Massively multiplex single-cell Hi-C

(2017) Vijay Ramani et al.   NATURE METHODS

Neuronal activity modifies the chromatin accessibility landscape in the adult brain

(2017) Yijing Su et al.   NATURE NEUROSCIENCE

Engrams and circuits crucial for systems consolidation of a memory

(2017) Takashi Kitamura et al.   SCIENCE

Thirst-associated preoptic neurons encode an aversive motivational drive

(2017) William E. Allen et al.   SCIENCE

Manipulation of nuclear architecture through CRISPR-mediated chromosomal looping

(2017) Stefanie L. Morgan et al.   Nature Communications

An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

(2017) Peter J Skene et al.   eLife

Memory retrieval by activating engram cells in mouse models of early Alzheimer’s disease

(2016) Dheeraj S. Roy et al.   NATURE

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

The molecular hallmarks of epigenetic control

(2016) C. David Allis et al.   NATURE REVIEWS GENETICS

Nuclear RNA-seq of single neurons reveals molecular signatures of activation

(2016) Benjamin Lacar et al.   Nature Communications

A robust activity marking system for exploring active neuronal ensembles

(2016) Andreas T Sørensen et al.   eLife

RNA sequencing from neural ensembles activated during fear conditioning in the mouse temporal association cortex

(2016) Jin-Hyung Cho et al.   Scientific Reports

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state

(2015) Assaf Rotem et al.   NATURE BIOTECHNOLOGY

DNA methylation changes in plasticity genes accompany the formation and maintenance of memory

(2015) Rashi Halder et al.   NATURE NEUROSCIENCE

Development of an intein-mediated split–Cas9 system for gene therapy

(2015) Dong-Jiunn Jeffery Truong et al.   NUCLEIC ACIDS RESEARCH

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

Engram cells retain memory under retrograde amnesia

(2015) T. J. Ryan et al.   SCIENCE

ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo

(2015) Gabriel E. Zentner et al.   Nature Communications

Epigenetic memory: the Lamarckian brain

(2014) A. Fischer   EMBO JOURNAL

Synaptic Plasticity Associated with a Memory Engram in the Basolateral Amygdala

(2014) A. Nonaka et al.   JOURNAL OF NEUROSCIENCE

Histone H2A.Z subunit exchange controls consolidation of recent and remote memory

(2014) Iva B. Zovkic et al.   NATURE

Bidirectional switch of the valence associated with a hippocampal contextual memory engram

(2014) Roger L. Redondo et al.   NATURE

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

(2014) Sébastien A Smallwood et al.   NATURE METHODS

Locus-specific epigenetic remodeling controls addiction- and depression-related behaviors

(2014) Elizabeth A Heller et al.   NATURE NEUROSCIENCE

Hippocampal Memory Traces Are Differentially Modulated by Experience, Time, and Adult Neurogenesis

(2014) Christine A. Denny et al.   NEURON

Can changes in histone acetylation contribute to memory formation?

(2014) Jose P. Lopez-Atalaya et al.   TRENDS IN GENETICS

The Regulation of Transcription in Memory Consolidation

(2014) Cristina M. Alberini et al.   Cold Spring Harbor Perspectives in Biology

Functional labeling of neurons and their projections using the synthetic activity–dependent promoter E-SARE

(2013) Takashi Kawashima et al.   NATURE METHODS

The Emerging Field of Neuroepigenetics

(2013) J. David Sweatt   NEURON

Permanent Genetic Access to Transiently Active Neurons via TRAP: Targeted Recombination in Active Populations

(2013) Casey J. Guenthner et al.   NEURON

Creating a False Memory in the Hippocampus

(2013) S. Ramirez et al.   SCIENCE

HDAC4 Governs a Transcriptional Program Essential for Synaptic Plasticity and Memory

(2012) Richard Sando et al.   CELL

Optogenetic stimulation of a hippocampal engram activates fear memory recall

(2012) Xu Liu et al.   NATURE

OPERating ON Chromatin, a Colorful Language where Context Matters

(2011) Kathryn E. Gardner et al.   JOURNAL OF MOLECULAR BIOLOGY

Neuronal activity modifies the DNA methylation landscape in the adult brain

(2011) Junjie U Guo et al.   NATURE NEUROSCIENCE

Spine growth in the anterior cingulate cortex is necessary for the consolidation of contextual fear memory

(2011) G. Vetere et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cortical DNA methylation maintains remote memory

(2010) Courtney A Miller et al.   NATURE NEUROSCIENCE

CREB's control of intrinsic and synaptic plasticity: implications for CREB-dependent memory models

(2010) Eva Benito et al.   TRENDS IN NEUROSCIENCES

Epigenetic influences on brain development and plasticity

(2009) Michela Fagiolini et al.   CURRENT OPINION IN NEUROBIOLOGY

HDAC2 negatively regulates memory formation and synaptic plasticity

(2009) Ji-Song Guan et al.   NATURE

Selective Erasure of a Fear Memory

(2009) J.-H. Han et al.   SCIENCE

In vivo and in vitro visualization of gene expression dynamics over extensive areas of the brain

(2008) M EGUCHI et al.   NEUROIMAGE

DNA methylation and histone acetylation work in concert to regulate memory formation and synaptic plasticity

(2007) Courtney A. Miller et al.   NEUROBIOLOGY OF LEARNING AND MEMORY