Endogenous miRNA sponges mediate the generation of oscillatory dynamics for a non-coding RNA network
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Abstract
Oscillations are crucial to the normal function of living organisms, across a wide variety of biological processes. In eukaryotes, oscillatory dynamics are thought to arise from interactions at the protein and RNA levels; however, the role of non-coding RNA in regulating these dynamics remains understudied. In this work, we show how non-coding RNA acting as microRNA (miRNA) sponges in a conserved miRNA - transcription factor feedback motif, can give rise to oscillatory behaviour, and how to test for this experimentally. Control of these non-coding RNA can dynamically create oscillations or stability, and we show how this behaviour predisposes to oscillations in the stochastic limit. These results, supported by emerging evidence for the role of miRNA sponges in development, point towards key roles of different species of miRNA sponges, such as circular RNA, potentially in the maintenance of yet unexplained oscillatory behaviour. These results help to provide a paradigm for understanding functional differences between the many redundant, but distinct RNA species thought to act as miRNA sponges in nature, such as long non-coding RNA, pseudogenes, competing mRNA, circular RNA, and3' UTRs.
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Cites
Global quantification of mammalian gene expression control
Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., & Selbach, M. (2011) · Nature · doi:10.1038/nature10098 · Cited by 6,566 · see citing works
Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function
Piwecka, M., Glažar, P., Hernandez-Miranda, L. R., Memczak, S., Wolf, S. A., Rybak-Wolf, A., Filipchyk, A., Klironomos, F., Cerda Jara, C. A., Fenske, P., et al. (2017) · Science · doi:10.1126/science.aam8526 · Cited by 1,210 · see citing works
Enuka, Y., Lauriola, M., Feldman, M. E., Sas-Chen, A., Ulitsky, I., & Yarden, Y. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1367 · Cited by 757 · see citing works
A Complex Oscillating Network of Signaling Genes Underlies the Mouse Segmentation Clock
Dequéant, M.-L., Glynn, E., Gaudenz, K., Wahl, M., Chen, J., Mushegian, A., & Pourquié, O. (2006) · Science · doi:10.1126/science.1133141 · Cited by 460 · see citing works
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- Authors
- Dhawan, A., Harris, A. L., Buffa, F. M., & Scott, J. G.
- Affiliations
- University of Oxford (GB)
- Cleveland Clinic (US)
- Corresponding author
- Scott, Jacob G.
- Venue
- Journal of Theoretical Biology
- Publisher
- Elsevier BV
- Published
- 2019-11
- Volume
- 481
- Pages
- 54-60
- ISSN
- 0022-5193 (ISSN-L)
- OpenAlex
- W2949304353
- Cited by
- 6
- References
- 4
- Citations by year
- 2026: 1 · 2023: 2 · 2022: 1 · 2021: 1 · 2020: 1
- FWCI
- 0.17
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nc-nd
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- Locations
- Journal of Theoretical Biology (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Oxford University Research Archive (ORA) (University of Oxford) (acceptedVersion)
- Archivio istituzionale della Ricerca - Bocconi (submittedVersion)
- Funders
- Cancer Research UK (S_3470, 23969)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › MicroRNA in disease regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
- Keywords
- microRNA sponge, oscillatory dynamics, non-coding RNA, circular RNA, long non-coding RNA, pseudogenes, competing endogenous RNA, 3' untranslated region, stochastic dynamics, biological oscillations
- MeSH terms
- RNA, Circular, Biological Clocks, Gene Expression Regulation, Models, Genetic, MicroRNAs, Gene Regulatory Networks, RNA, Long Noncoding
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