Quantitative Modeling of MicroRNA:Target Interactions in Cell Fate Transition

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Quantitative Modeling of MicroRNA:Target Interactions in Cell Fate Transition Project Summary Cell fate transition is one of the most fundamental processes in biology. Such a transition is often thought to involve the coordinated action of multiple genes. MicroRNAs (miRNAs), an abundant class of small non-coding RNAs, have been postulated as key regulators of cell fate transition. However, complete elucidation of miRNA-mediated gene regulation has been a major challenge, and thus the current understanding of the roles and mechanisms of miRNAs during cell fate transition processes is limited. MiRNAs recognize their messenger RNA (mRNA) targets predominantly through binding sites in the 3ʹ′ untranslated regions (3ʹ′ UTRs). Successful target binding leads to mRNA degradation and/or translational repression. The regulatory outcome on a miRNA target is greatly influenced by the miRNA abundance and sponges, which are RNAs that compete with the target for interaction with the miRNA. These two important factors, and quantitative modeling of seedless site contributions and miRNA:target interactions have been completely ignored by existing miRNA target prediction algorithms. To address these algorithmic limitations for complete elucidation of miRNA regulatory functions, the interdisciplinary research team will 1) quantitatively map miRNA-mediated regulation of key regulators of cell fate transition, and measure miRNA and mRNA expression by next-generation sequencing; 2) develop a novel modeling framework that can address combined effects of seed and seedless sites and incorporate miRNA abundance and sponge effects for quantitative modeling of miRNA:target interactions; 3) predict  miRNA-mediated targeting during induced pluripotent stem cell fate transition; 4) validate miRNA- regulated targeting in cell fate transition and test predicted effects of seedless sites and miRNA and sponge abundance; and 5) disseminate results through database and software tools. This project will result in novel models for quantitative modeling of miRNA:target interactions that can address the effects of both seed and seedless sites, miRNA abundance and sponges. The model can be broadly applicable beyond the context of cell fate transition. The project will also lead to the identification of previously unknown miRNA-targeted genes, and provide key mechanistic insights into the miRNA- regulated control of cell fate transition. This research will significantly advance understanding of miRNA- mediated gene regulation in human development, facilitate development of miRNA-oriented therapeutics, and benefit human health.