Quantitative Characteristic of ncRNA Regulation in Gene Regulatory Networks

  • Federico Bocci
  • Mohit Kumar Jolly
  • Herbert LevineEmail author
  • José Nelson OnuchicEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1912)


RNA is mostly known for its role in protein synthesis, where it encodes information for protein sequence in its messenger RNA (mRNA) form (translation). Yet, RNA molecules regulate several cellular processes other than translation. Here, we present an overview of several mathematical models that help understanding and characterizing the role of noncoding RNA molecules (ncRNAs) in regulating gene expression and protein synthesis. First, we discuss relatively simple models where ncRNAs can modulate protein synthesis via targeting a mRNA. Then, we consider the case of feedback interactions between ncRNAs and their target proteins, and discuss several biological applications where these feedback architectures modulate a cellular phenotype and control the levels of intrinsic and extrinsic noise. Building from these simple circuit motifs, we examine feed-forward circuit motifs involving ncRNAs that generate precise spatial and temporal patterns of protein expression. Further, we investigate the competition between ncRNAs and other endogenous RNA molecules and show that the cross talk between coding and noncoding RNAs can form large genetic circuits that involve up to hundreds of chemical species. Finally, we discuss the role of ncRNAs in modulating cell-cell signaling pathways and therefore the dynamics of spatiotemporal pattern formation in a tissue.

Key words

Noncoding RNA Gene network Mathematical model Network motif Feedback loops 


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© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Center for Theoretical Biological PhysicsRice UniversityHoustonUSA
  2. 2.Department of ChemistryRice UniversityHoustonUSA
  3. 3.Department of BioengineeringRice UniversityHoustonUSA
  4. 4.Department of Physics and AstronomyRice UniversityHoustonUSA
  5. 5.Department of BiosciencesRice UniversityHoustonUSA

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