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Kinetic Modelling of Competition and Depletion of Shared miRNAs by Competing Endogenous RNAs

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Computational Biology of Non-Coding RNA

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1912))

Abstract

Non-coding RNAs play a key role in the post-transcriptional regulation of mRNA translation and turnover in eukaryotes. miRNAs, in particular, interact with their target RNAs through protein-mediated, sequence-specific binding, giving rise to extended and highly heterogeneous miRNA–RNA interaction networks. Within such networks, competition to bind miRNAs can generate an effective positive coupling between their targets. Competing endogenous RNAs (ceRNAs) can in turn regulate each other through miRNA-mediated crosstalk. Albeit potentially weak, ceRNA interactions can occur both dynamically, affecting, e.g., the regulatory clock, and at stationarity, in which case ceRNA networks as a whole can be implicated in the composition of the cell’s proteome. Many features of ceRNA interactions, including the conditions under which they become significant, can be unraveled by mathematical and in silico models. We review the understanding of the ceRNA effect obtained within such frameworks, focusing on the methods employed to quantify it, its role in the processing of gene expression noise, and how network topology can determine its reach.

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Acknowledgements

Work supported by the European Union’s Horizon 2020 research and innovation programme MSCA-RISE-2016 under grant agreement No 734439 INFERNET. We are indebted with Matteo Figliuzzi, Enzo Marinari, Matteo Marsili and Riccardo Zecchina for our fruitful and enjoyable collaboration.

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Authors and Affiliations

  1. Laboratory of Glia Biology, VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium

    Araks Martirosyan

  2. KU Leuven, Department of Neuroscience, Leuven, Belgium

    Araks Martirosyan

  3. DISAT, Politecnico di Torino, Turin, Italy

    Marco Del Giudice, Chiara Enrico Bena, Andrea Pagnani & Carla Bosia

  4. Italian Institute for Genomic Medicine, Turin, Italy

    Marco Del Giudice, Chiara Enrico Bena, Andrea Pagnani & Carla Bosia

  5. Soft & Living Matter Lab, CNR-NANOTEC, Rome, Italy

    Andrea De Martino

  6. Italian Institute for Genomic Medicine, Turin, Italy

    Andrea De Martino

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  1. Araks Martirosyan
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  2. Marco Del Giudice
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  3. Chiara Enrico Bena
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  4. Andrea Pagnani
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  5. Carla Bosia
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  6. Andrea De Martino
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Corresponding author

Correspondence to Andrea De Martino .

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Editors and Affiliations

  1. Department of Dermatology, Erlangen University Hospital, Erlangen, Germany

    Xin Lai

  2. Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany

    Shailendra K. Gupta

  3. Department of Dermatology, Erlangen University Hospital, Erlangen, Germany

    Julio Vera

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Martirosyan, A., Del Giudice, M., Bena, C.E., Pagnani, A., Bosia, C., De Martino, A. (2019). Kinetic Modelling of Competition and Depletion of Shared miRNAs by Competing Endogenous RNAs. In: Lai, X., Gupta, S., Vera, J. (eds) Computational Biology of Non-Coding RNA. Methods in Molecular Biology, vol 1912. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8982-9_15

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  • DOI: https://doi.org/10.1007/978-1-4939-8982-9_15

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