Letter abstract

Nature Genetics 39, 1278 - 1284 (2007)
Published online: 23 September 2007 | doi:10.1038/ng2135

The role of site accessibility in microRNA target recognition

Michael Kertesz1,3, Nicola Iovino2,3, Ulrich Unnerstall2, Ulrike Gaul2,3 & Eran Segal1,3


MicroRNAs are key regulators of gene expression1, 2, 3, 4, but the precise mechanisms underlying their interaction with their mRNA targets are still poorly understood. Here, we systematically investigate the role of target-site accessibility, as determined by base-pairing interactions within the mRNA, in microRNA target recognition. We experimentally show that mutations diminishing target accessibility substantially reduce microRNA-mediated translational repression, with effects comparable to those of mutations that disrupt sequence complementarity. We devise a parameter-free model for microRNA-target interaction that computes the difference between the free energy gained from the formation of the microRNA-target duplex and the energetic cost of unpairing the target to make it accessible to the microRNA. This model explains the variability in our experiments, predicts validated targets more accurately than existing algorithms, and shows that genomes accommodate site accessibility by preferentially positioning targets in highly accessible regions. Our study thus demonstrates that target accessibility is a critical factor in microRNA function.

  1. Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel.
  2. Laboratory of Developmental Neurogenetics, Rockefeller University, New York, New York 10021, USA.
  3. These authors contributed equally to this work.

Correspondence to: Ulrike Gaul2,3 e-mail: gaul@mail.rockefeller.edu

Correspondence to: Eran Segal1,3 e-mail: eran@weizmann.ac.il


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