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Impulse Control: Temporal Dynamics in Gene Transcription
Abstract
Regulatory circuits controlling gene expression constantly rewire to adapt to environmental stimuli, differentiation cues, and disease. We review our current understanding of the temporal dynamics of gene expression in eukaryotes and prokaryotes and the molecular mechanisms that shape them. We delineate several prototypical temporal patterns, including ‘impulse’ (single-pulse) patterns in response to transient environmental stimuli, sustained (state transitioning) patterns in response to developmental cues, and oscillating patterns. We focus on impulse responses and their higher-order temporal organization in regulons and cascades, and describe how core protein circuits and cis-regulatory sequences in promoters integrate with chromatin architecture to generate these responses.
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“By contrast, expression and epigenetic changes controlled by the GRN usually happen over a scale of minutes to hours or even days (63, 64).”
From Behavior-related gene regulatory networks: A new level of organization in the brain (2020) · cites this paper as [63]
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Jovanovic, M., Rooney, M. S., Mertins, P., Przybylski, D., Chevrier, N., Satija, R., Rodriguez, E. H., Fields, A. P., Schwartz, S., Raychowdhury, R., et al. (2015) · Science · doi:10.1126/science.1259038 · Cited by 460
Self-citationRam, O., Goren, A., Amit, I., Shoresh, N., Yosef, N., Ernst, J., Kellis, M., Gymrek, M., Issner, R., Coyne, M., et al. (2011) · Cell · doi:10.1016/j.cell.2011.09.057 · Cited by 331
Self-citation
Metadata
- Authors
- Yosef, N., & Regev, A.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2011-03
- Volume
- 144
- Issue
- 6
- Pages
- 886-896
- ISSN
- 0092-8674
- PMC
- PMC3148525
- Cited by
- 258
- References
- 102
- Language
- en
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 869 d)
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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Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.