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Unraveling the determinants of microRNA mediated regulation using a massively parallel reporter assay

Author

Listed:
  • Ilya Vainberg Slutskin

    (Weizmann Institute of Science
    Weizmann Institute of Science)

  • Shira Weingarten-Gabbay

    (Weizmann Institute of Science
    Weizmann Institute of Science)

  • Ronit Nir

    (Weizmann Institute of Science
    Weizmann Institute of Science)

  • Adina Weinberger

    (Weizmann Institute of Science
    Weizmann Institute of Science)

  • Eran Segal

    (Weizmann Institute of Science
    Weizmann Institute of Science)

Abstract

Despite extensive research, the sequence features affecting microRNA-mediated regulation are not well understood, limiting our ability to predict gene expression levels in both native and synthetic sequences. Here we employed a massively parallel reporter assay to investigate the effect of over 14,000 rationally designed 3′ UTR sequences on reporter construct repression. We found that multiple factors, including microRNA identity, hybridization energy, target accessibility, and target multiplicity, can be manipulated to achieve a predictable, up to 57-fold, change in protein repression. Moreover, we predict protein repression and RNA levels with high accuracy (R = 0.84 and R = 0.80, respectively) using only 3′ UTR sequence, as well as the effect of mutation in native 3′ UTRs on protein repression (R = 0.63). Taken together, our results elucidate the effect of different sequence features on miRNA-mediated regulation and demonstrate the predictability of their effect on gene expression with applications in regulatory genomics and synthetic biology.

Suggested Citation

  • Ilya Vainberg Slutskin & Shira Weingarten-Gabbay & Ronit Nir & Adina Weinberger & Eran Segal, 2018. "Unraveling the determinants of microRNA mediated regulation using a massively parallel reporter assay," Nature Communications, Nature, vol. 9(1), pages 1-18, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-02980-z
    DOI: 10.1038/s41467-018-02980-z
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    Cited by:

    1. Ting Fu & Kofi Amoah & Tracey W. Chan & Jae Hoon Bahn & Jae-Hyung Lee & Sari Terrazas & Rockie Chong & Sriram Kosuri & Xinshu Xiao, 2024. "Massively parallel screen uncovers many rare 3′ UTR variants regulating mRNA abundance of cancer driver genes," Nature Communications, Nature, vol. 15(1), pages 1-20, December.

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