The DOI matches its Crossref record; 178 of the 178 references it cites were found in a registry or an index.
Different Neuronal Activity Patterns Induce Different Gene Expression Programs
Open accessPublished version of a preprint
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“whereas maximum Bdnf upregulation occurred after 6 h”
From Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression (2020) · cites this paper as [9]
In the citing paper
“we re-analyzed a recently published RNA-seq time course during pharmacological neuronal activation9 and found maximum activation of the IEGs Fos and Arc by 60 min”
From Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression (2020) · cites this paper as [9]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
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
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
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
Flagged first, then by citations
Cited by
Sorted by citations
Activity-Regulated Transcription: Bridging the Gap between Neural Activity and Behavior
Yap, E.-L., & Greenberg, M. E. (2018) · Neuron · doi:10.1016/j.neuron.2018.10.013 · Cited by 706
Diversity and Emerging Roles of Enhancer RNA in Regulation of Gene Expression and Cell Fate
Arnold, P. R., Wells, A. D., & Li, X. C. (2020) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2019.00377 · Cited by 259
METTL3-mediated N6-methyladenosine mRNA modification enhances long-term memory consolidation
Zhang, Z., Wang, M., Xie, D., Huang, Z., Zhang, L., Yang, Y., Ma, D., Li, W., Zhou, Q., Wang, X., et al. (2018) · Cell Research · doi:10.1038/s41422-018-0092-9 · Cited by 211
Early Alzheimer’s disease pathology in human cortex involves transient cell states
Gazestani, V., Kamath, T., Nadaf, N. M., Dougalis, A., Burris, S. J., Rooney, B., Junkkari, A., Vanderburg, C., Pelkonen, A., Gomez-Budia, M., et al. (2023) · Cell · doi:10.1016/j.cell.2023.08.005 · Cited by 209
The molecular cytoarchitecture of the adult mouse brain
Langlieb, J., Sachdev, N., Balderrama, K. S., Nadaf, N. M., Raj, M., Murray, E. M., Webber, J. T., Vanderburg, C. R., Gazestani, V., Tward, D. J., et al. (2023) · Nature · doi:10.1038/s41586-023-06818-7 · Cited by 252
Metadata
- 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
- Venue
- Neuron
- Publisher
- Elsevier BV
- Published
- 2018-05
- Volume
- 98
- Issue
- 3
- Pages
- 530-546.e11
- ISSN
- 0896-6273 (ISSN-L)
- 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
- 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
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 ›
Are you an author, or do you see a problem with this page? Request a review
