MicroRNA 3′-compensatory pairing occurs through two binding modes, with affinity shaped by nucleotide identity and position
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, United States
Abstract
MicroRNAs (miRNAs), in association with Argonaute (AGO) proteins, direct repression by pairing to sites within mRNAs. Compared to pairing preferences of the miRNA seed region (nucleotides 2-8), preferences of the miRNA 3′ region are poorly understood, due to the sparsity of measured affinities for the many pairing possibilities. We used RNA bind-n-seq with purified AGO2-miRNA complexes to measure relative affinities of >1,000 3′-pairing architectures for each miRNA. In some cases, optimal 3′ pairing increased affinity by >500-fold. Some miRNAs had two high-affinity 3′-pairing modes-one of which included additional nucleotides bridging seed and 3′ pairing to enable high-affinity pairing to miRNA nucleotide 11. The affinity of binding and the position of optimal pairing both tracked with the occurrence of G or oligo(G/C) nucleotides within the miRNA. These and other results advance understanding of miRNA targeting, providing insight into how optimal 3′ pairing is determined for each miRNA.
Data availability
Sequencing data have been deposited in GEO; accession GSE196458, and can be accessed with the reviewer token mtotysyidzwptef.
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The biochemical basis of microRNA targeting efficacyNCBI Gene Expression Omnibus, GSE140220.
Article and author information
Author details
Funding
National Institute of General Medical Sciences (GM118135)
- David P Bartel
National Institute of General Medical Sciences (GM123719)
- Namita Bisaria
Howard Hughes Medical Institute
- David P Bartel
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2022, McGeary et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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MicroRNA 3′-compensatory pairing occurs through two binding modes, with affinity shaped by nucleotide identity and position
eLife 11:e69803.
https://doi.org/10.7554/eLife.69803
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