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A Roadmap for the Computational Prediction and Experimental Validation of Competitive Endogenous RNAs

  • Florian A. KarrethEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1970)

Abstract

MicroRNAs (miRNAs) are fine-tuners of gene expression and contribute to the regulation of most, if not all, biological processes in eukaryotes by targeting both coding and noncoding RNAs. Typically, miRNAs repress numerous target transcripts and most target RNAs harbor binding sites for multiple miRNA families. It was recently proposed that transcripts sequester miRNAs and thereby regulate the abundance of other transcripts with which they have miRNA binding sites in common. Since competition for shared miRNAs is the mechanistic basis for this cross-regulation, such transcripts were termed competitive endogenous RNAs (ceRNAs). In this chapter, I discuss considerations for the computational prediction of ceRNAs based on miRNA binding site overlap. Moreover, I provide a framework for the experimental validation of miRNA-dependent reciprocal regulation of putative ceRNAs.

Key words

MicroRNA Competitive endogenous RNA Natural miRNA sponge miRNA cross-regulation 

Notes

Acknowledgments

I thank the members of my laboratory for critical reading of the manuscript. This work was partially supported by a K22 Career Development Award (1K22CA197058-01) and a project grant (1R03CA227349-01) from the NCI/NIH, and a Young Investigator Award from the Melanoma Research Alliance.

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Copyright information

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

Authors and Affiliations

  1. 1.Department of Molecular OncologyH. Lee Moffitt Cancer Center and Research InstituteTampaUSA

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