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Efficient 3'-pairing renders microRNA targeting less sensitive to mRNA seed accessibility

David M Kosek1, Elnaz Banijamali2, Walter Becker2

  • 1Department of Cell and Molecular Biology, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177Stockholm, Sweden.

Nucleic Acids Research
|October 11, 2023
PubMed

Insights

MicroRNAs (miRNAs) use 3'-pairing to target mRNAs, even when seed regions are inaccessible. This interaction enhances gene silencing efficiency and improves miRNA target prediction models.

Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • MicroRNAs (miRNAs) regulate gene expression post-transcriptionally.
  • miRNA target recognition primarily involves the seed region (nucleotides 2-8).
  • 3 -pairing, beyond the seed region, also influences miRNA:target interactions.

Purpose of the Study:

  • To investigate the combined effects of 3 -pairing and mRNA secondary structures on miRNA repression efficiency.
  • To provide structural and functional evidence for 3 -pairing's role in overcoming seed-binding site inaccessibility.
  • To refine predictions of effective miRNA target sites.

Main Methods:

  • Selective 2 -hydroxyl acylation analyzed by primer extension (SHAPE) to study RNA structures.
  • Luciferase reporter assays to measure gene repression efficiency.
  • Transcriptomics analyses and high-throughput modeling of 3 -untranslated regions (3 -UTRs).

Main Results:

  • 3 -pairing can compensate for inaccessible seed-binding sites, enabling miRNA-mediated repression.
  • miRNA 3 -pairing can interact with mRNA sequences upstream of the seed site.
  • Hairpins and bulges in target sites are tolerated, and SHAPE confirms predicted structures for effective 3 -pairing.
  • Inaccessible targets like PHB2 (miR-141) can be effectively repressed through 3 -pairing.

Conclusions:

  • 3 -pairing is a significant factor in miRNA target recognition, especially for sites with low seed accessibility.
  • The study provides a refined model for predicting miRNA target efficacy.
  • Understanding 3 -pairing enhances our knowledge of post-transcriptional gene regulation by miRNAs.

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