Cited by 399Neuroscience and Neuropharmacology ResearchMemory and Neural MechanismsNeural dynamics and brain function

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Different Neuronal Activity Patterns Induce Different Gene Expression Programs

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Tyssowski, Kelsey M., DeStefino, Nicholas R., Cho, Jin-Hyung, Dunn, Carissa J., Poston, Robert G., Carty, Crista E., Jones, Richard D., Chang, Sarah M., Romeo, Palmyra, Wurzelmann, Mary K., Ward, James M., Andermann, Mark L., Saha, Ramendra N., Dudek, Serena M., Gray, Jesse M.·2018·Neuron

DOI 10.1016/j.neuron.2018.04.001PMC PMC5934296

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Abstract

A vast number of different neuronal activity patterns could each induce a different set of activity-regulated genes. Mapping this coupling between activity pattern and gene induction would allow inference of a neuron's activity-pattern history from its gene expression and improve our understanding of activity-pattern-dependent synaptic plasticity. In genome-scale experiments comparing brief and sustained activity patterns, we reveal that activity-duration history can be inferred from gene expression profiles. Brief activity selectively induces a small subset of the activity-regulated gene program that corresponds to the first of three temporal waves of genes induced by sustained activity. Induction of these first-wave genes is mechanistically distinct from that of the later waves because it requires MAPK/ERK signaling but does not require de novo translation. Thus, the same mechanisms that establish the multi-wave temporal structure of gene induction also enable different gene sets to be induced by different activity durations.

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The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
STAR: ultrafast universal RNA-seq aligner
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709
<tt>edgeR</tt> : a Bioconductor package for differential expression analysis of digital gene expression data
Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp616 · Cited by 41,364
Matplotlib: a 2D graphics environment
Hunter, J. D. (2007) · Computing in Science & Engineering · doi:10.1109/mcse.2007.55 · Cited by 39,249
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
Calcium's Role in Mechanotransduction during Muscle Development
Damm, T. B., & Egli, M. (2014) · Cellular Physiology and Biochemistry · doi:10.1159/000356667 · Cited by 14,552
The NumPy Array: A Structure for Efficient Numerical Computation
van der Walt, S., Colbert, S. C., & Varoquaux, G. (2011) · Computing in Science & Engineering · doi:10.1109/mcse.2011.37 · Cited by 9,381
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
Trapnell, C., Cacchiarelli, D., Grimsby, J., Pokharel, P., Li, S., Morse, M., Lennon, N. J., Livak, K. J., Mikkelsen, T. S., & Rinn, J. L. (2014) · Nature Biotechnology · doi:10.1038/nbt.2859 · Cited by 7,314

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Periandri, E. M., Dodson, K. M., Vitorino, F. N. D. L., Garcia, B. A., Glastad, K. M., & Egervári, G. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.08.26.609729 · Cited by 2
Muti-omics characterization reveals brain-wide disruption of synapses and region- and age-specific changes in neurons and glia in Sp4 mutant mice, a genetic model of schizophrenia and bipolar disorderPreprint
Kwon, M. J., Mandell, K. A. P., Aryal, S., Geng, C., Nicolella, A. A., Valle-Tojeiro, A., Natarajan, S., Misri, D., Hall, A., Song, B. J., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.12.618006 · Cited by 2
Epigenetic changes, neuronal dysregulation and metabolomic abnormalities in Zmym2 mutant mice, a genetic model of schizophrenia and neurodevelopmental disordersPreprint
Huang, W.-C., Mandell, K. A. P., Aryal, S., Song, B. J., Valle-Tojeiro, A., Goble, N., Geng, C., Asan, A. S., Liu, X., Dennis, C., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.02.18.638656 · Cited by 2
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Arai, M., Osanai, H., Snell, C. C., 北村, 貴., & Ogawa, S. K. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.21.649441 · Cited by 2
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Nakayama, K., Mubuchi, A., & Miyata, S. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.29.656756 · Cited by 2
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Sepahvand, T., Qin, T., Hasan, Z., Power, K. D., Carew, S. J., Nazari, N., Janes, A. M., Salman, A., Xia, Y., Benoukraf, T., et al. (2025) · Communications Biology · doi:10.1038/s42003-025-08287-2 · Cited by 1
Neuronal activity-dependent gene expression is stimulus-specific and changes with neuronal maturation
Lukin, J., Beckel, M. S., Pedroncini, O., Giusti, S. A., Mauro, G. C. D., Linenberg, I. M., Patop, I. L., Chernomoretz, A., Marín‐Burgin, A., Kadener, S., et al. (2025) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2025.1609772 · Cited by 2
The effects of electrical stimulation on neurons and glia of the central nervous system
Devlin, J., & Gilbert, R. J. (2025) · Journal of Neural Engineering · doi:10.1088/1741-2552/ae2f9c · Cited by 1
In vivo two-photon imaging reveals stochastic and synchronized extracellular signal-regulated kinase dynamics in neurons of awake mice
Zeybek, C., Kondo, Y., Matsuda, M., & Yukinaga, H. (2026) · Neuroscience Research · doi:10.1016/j.neures.2026.105032 · Cited by 1
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Zhao, Q., Li, Y., Zhang, J., Gao, K., Shi, L., Liu, E., Yang, W., Zhang, T., Mei, X., & Shen, Z. (2026) · Regenerative Biomaterials · doi:10.1093/rb/rbag039 · Cited by 1
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Xu, Z., Xu, C., Wang, Q., Ma, S., Li, Y., Liu, S., Peng, S., Tan, J., Zhao, X., Han, D., et al. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2022.979542 · Cited by 1
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Zea-Redondo, L., & Pombo, A. (2022) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2022.100443 · Cited by 1
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Jiang, J., Liu, S., Xu, Z., Yu, S., Wang, L., Long, S., Ye, S., Yan, Y., Xu, H., Zhang, J., et al. (2024) · ACS Chemical Neuroscience · doi:10.1021/acschemneuro.4c00047 · Cited by 2
Nature and Nurture Converge in the Nucleus to Regulate Activity-Dependent Neuronal Development
Thompson, J. R., & Lin, Y. (2024) · Springer eBooks · doi:10.1007/978-3-031-68550-7_10 · Cited by 1
Higher-Order Genome Organization in the Control of Neuronal Identity and Neural Circuit Plasticity
Yamada, T., Valnegri, P., & Yang, Y. (2024) · Springer eBooks · doi:10.1007/978-3-031-68550-7_8 · Cited by 1
Gene Regulation by Nuclear Calcium and Its Antagonism by NMDAR/TRPM4 Signaling
Pruunsild, P., Bengtson, C. P., Yan, J., Bading, H., & Hagenston, A. M. (2024) · Springer eBooks · doi:10.1007/978-3-031-68550-7_4 · Cited by 1
Topological influence of immediate-early genes in brain genetic networks and their link to Alzheimer's disease
Zachariou, M., Loizidou, E. M., & Spyrou, G. M. (2025) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2025.110043 · Cited by 3
Bulk-based hypothesis weighing increases power in single-cell differential expression analysis
Germain, P., Wang, J., & Robinson, M. D. (2025) · Peer Community Journal · doi:10.24072/pcjournal.663 · Cited by 1
Specific Functions of ERK/MAPK Signaling in Brain Development and Neurocognition
Holter, M. C. (2019) · Cited by 1
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Hu, G., Lee, V. D., Lin, H., Mao, P.-W., Liu, H., Peh, J.-H., & Chen, C. (2021) · Springer eBooks · doi:10.1007/978-981-10-8953-4_10 · Cited by 1
Setting the pace
Lewis, S. (2018) · Nature reviews. Neuroscience · doi:10.1038/s41583-018-0022-3 · Cited by 1
The activity-dependent transcription factor Npas4 regulates IQSEC3 expression in somatostatin interneurons to mediate anxiety-like behaviorPreprint
Kim, S., Park, D., Kim, J., Lee, D., Kim, D., Kim, H., Hong, S., Jeon, J., Kim, J., Cheong, E., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/659805 · Cited by 1
Comparative chromatin accessibility upon BDNF-induced neuronal activity delineates neuronal regulatory elementsPreprint
Ibarra, I. L., Ratnu, V. S., Gordillo, L., Hwang, I., Mariani, L., Weinand, K., Hammarén, H. M., Bulyk, M. L., Savitski, M. M., Zaugg, J. B., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.28.446128 · Cited by 1

Authors: Tyssowski, K. M., DeStefino, N. R., Cho, J.-H., Dunn, C. J., Poston, R. G., Carty, C. E., Jones, R. D., Chang, S. M., Romeo, P., Wurzelmann, M. K., Ward, J. M., Andermann, M. L., Saha, R. N., Dudek, S. M., & Gray, J. M.
Affiliations: Harvard University (US)
University of California, Merced (US)
Beth Israel Deaconess Medical Center (US)
National Institute of Environmental Health Sciences (US)
National Institutes of Health (US)
Corresponding author: Saha, Ramendra N.
Dudek, Serena M.
Gray, Jesse M.
ORCID: Tyssowski, Kelsey M.
Dunn, Carissa J.
Jones, Richard D.
Chang, Sarah M.
Ward, James M.
Andermann, Mark L.
Saha, Ramendra N.
Dudek, Serena M.
Gray, Jesse M.
Venue: Neuron
Publisher: Elsevier BV
Published: 2018-05
Volume: 98
Issue: 3
Pages: 530-546.e11
ISSN: 0896-6273 (ISSN-L)
DOI: 10.1016/j.neuron.2018.04.001
PMC: PMC5934296
OpenAlex: W2950828985
Cited by: 390
References: 177
Citations by year: 2026: 39 · 2025: 51 · 2024: 67 · 2023: 54 · 2022: 50 · 2021: 41 · 2020: 39 · 2019: 34 · 2018: 14
FWCI: 14.57
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 366 d)
Locations: Neuron (publishedVersion)
bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
eScholarship (California Digital Library) (submittedVersion)
Funders: Armenise-Harvard (R01 MH101528-01, R01 MH116223-01)
Kaneb family
Intramural Research Program of the National Institute of Environmental Health Sciences
National Institutes of Health (Z01 ES100221)
NSF Graduate Research Fellowship Program (DGE1144152, DEG1745303)
National Institute of Health NRSA (R00 MH096941)
Canadian Institute of Health Research
NIH New Innovator Award (DP2 DK105570, R01 DK109930)
McKnight Scholar Award
Harvard Brain Science Initiative Bipolar Disorder Seed Grant
Topics: Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
Life Sciences › Neuroscience › Cognitive Neuroscience › Memory and Neural Mechanisms
Life Sciences › Neuroscience › Cognitive Neuroscience › Neural dynamics and brain function
Keywords: neural activity patterns, activity duration, ERK signaling, synaptic plasticity, gene expression profiling
MeSH terms: Animals, Cells, Cultured, Cerebral Cortex, Female, Gene Expression Regulation, Male, Mice, Inbred C57BL, Mice, Inbred ICR, Neurons, Photic Stimulation, Rats, Sprague-Dawley, MAP Kinase Signaling System, Mice, Rats

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Different Neuronal Activity Patterns Induce Different Gene Expression Programs

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