Immediate and deferred epigenomic signatures of in vivo neuronal activation in mouse hippocampus
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Abstract
Activity-driven transcription plays an important role in many brain processes, including those underlying memory and epilepsy. Here we combine genetic tagging of nuclei and ribosomes with RNA sequencing, chromatin immunoprecipitation with sequencing, assay for transposase-accessible chromatin using sequencing and Hi-C to investigate transcriptional and chromatin changes occurring in mouse hippocampal excitatory neurons at different time points after synchronous activation during seizure and sparse activation by novel context exploration. The transcriptional burst is associated with an increase in chromatin accessibility of activity-regulated genes and enhancers, de novo binding of activity-regulated transcription factors, augmented promoter-enhancer interactions and the formation of gene loops that bring together the transcription start site and transcription termination site of induced genes and may sustain the fast reloading of RNA polymerase complexes. Some chromatin occupancy changes and interactions, particularly those driven by AP1, remain long after neuronal activation and could underlie the changes in neuronal responsiveness and circuit connectivity observed in these neuroplasticity paradigms, perhaps thereby contributing to metaplasticity in the adult brain.
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The 3D genome is actively regulated during learning and memory formation.
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- Authors
- Fernandez-Albert, J., Lipinski, M., Lopez-Cascales, M. T., Rowley, M. J., Martin-Gonzalez, A. M., del Blanco, B., Corces, V. G., & Barco, A.
- Affiliations
- Emory University (US)
- Venue
- Nature Neuroscience
- Published
- 2019-09-09
- Volume
- 22
- Issue
- 10
- Pages
- 1718-1730
- ISSN
- 1097-6256 (ISSN-L)
- 1546-1726
- OpenAlex
- W2972344703
- Cited by
- 166
- References
- 81
- Citations by year
- 2026: 16 · 2025: 27 · 2024: 31 · 2023: 26 · 2022: 23 · 2021: 23 · 2020: 19 · 2019: 1
- FWCI
- 5.46
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Locations
- Nature Neuroscience (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion)
- Funders
- Ministerio de Economía y Competitividad (SVP-2014-068387, SAF2017-87928-R, SEV-2017-0723)
- U.S. Department of Health & Human Services | NIH | National Center for Research Resources (GM035463)
- Generalitat Valenciana (PROMETEO/2016/026)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Neuroscience › Cognitive Neuroscience › Memory and Neural Mechanisms
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
- Keywords
- neuronal activation, hippocampus, excitatory neurons, chromatin accessibility, enhancers, enhancer-promoter interactions, AP-1, metaplasticity, neuroplasticity, seizures, epigenomic signatures, chromatin occupancy
- MeSH terms
- Animals, Chromatin, Enhancer Elements, Genetic, Hippocampus, Male, Mice, Inbred C57BL, Neuronal Plasticity, Neurons, Promoter Regions, Genetic, Seizures, Status Epilepticus, Transcription, Genetic, Genes, Immediate-Early, Transcription Factor AP-1, Mice, Epigenomics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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