MicroRNA 3′-compensatory pairing occurs through two binding modes, with affinity shaped by nucleotide identity and position

Abstract
Data availability
Article and author information
Metrics

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.

The following data sets were generated

1. McGeary SE
2. Bisaria N
3. Pham TM
4. Wang PY
5. Bartel DP
(2022) MicroRNA 3′-compensatory pairing occurs through two binding modes, with affinity shaped by nucleotide identity and position
NCBI Gene Expression Omnibus, GSE196458.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE196458

The following previously published data sets were used

1. McGeary SE
2. Lin KS
3. Shi CY
4. Pham TM
5. Bisaria N
6. Bartel DP
(2019) The biochemical basis of microRNA targeting efficacy
NCBI Gene Expression Omnibus, GSE140220.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE140220

Article and author information

Author details

Sean E McGeary

Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-5343-6447
Namita Bisaria

Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States

Competing interests
The authors declare that no competing interests exist.
Thy M Pham

Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States

Competing interests
The authors declare that no competing interests exist.
Peter Y Wang

Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States

Competing interests
The authors declare that no competing interests exist.
David P Bartel

Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States

For correspondence
dbartel@wi.mit.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-3872-2856

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

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.