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Nat Commun. 2018 Jun 22;9(1):2430. doi: 10.1038/s41467-018-04575-0.

A mixed antagonistic/synergistic miRNA repression model enables accurate predictions of multi-input miRNA sensor activity.

Gam JJ1,2, Babb J1,2, Weiss R3,4.

Author information

1
Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA.
2
Synthetic Biology Center, MIT, Cambridge, MA, 02139, USA.
3
Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA. rweiss@mit.edu.
4
Synthetic Biology Center, MIT, Cambridge, MA, 02139, USA. rweiss@mit.edu.

Abstract

MicroRNAs (miRNAs) regulate a majority of protein-coding genes, affecting nearly all biological pathways. However, the quantitative dimensions of miRNA-based regulation are not fully understood. In particular, the implications of miRNA target site location, composition rules for multiple target sites, and cooperativity limits for genes regulated by many miRNAs have not been quantitatively characterized. We explore these aspects of miRNA biology at a quantitative single-cell level using a library of 620 miRNA sensors and reporters that are regulated by many miRNA target sites at different positions. Interestingly, we find that miRNA target site sets within the same untranslated region exhibit combined miRNA activity described by an antagonistic relationship while those in separate untranslated regions show synergy. The resulting antagonistic/synergistic computational model enables the high-fidelity prediction of miRNA sensor activity for sensors containing many miRNA targets. These findings may help to accelerate the development of sophisticated sensors for clinical and research applications.

PMID:
29934631
PMCID:
PMC6014984
DOI:
10.1038/s41467-018-04575-0
[Indexed for MEDLINE]
Free PMC Article

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