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bioRxiv · 10.1101/2021.04.13.439700

Pairing to the microRNA 3' region occurs through two alternative binding modes, with affinity shaped by nucleotide identity as well as pairing position

McGeary, S. E.·Bisaria, N.·Bartel, D. P.
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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. HIGHLIGHTSO_LIRNA bind-n-seq reveals relative affinities of >1,000 3'-pairing architectures C_LIO_LITwo distinct 3'-binding modes can enhance affinity, by >500-fold in some instances C_LIO_LIG and oligo(G/C) residues help define the miRNA 3' segment most critical for pairing C_LIO_LISeed mismatch identity can influence the contribution of compensatory 3' pairing C_LI

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McGeary, S. E., Bisaria, N., Bartel, D. P.. 2021-04-14. Pairing to the microRNA 3' region occurs through two alternative binding modes, with affinity shaped by nucleotide identity as well as pairing position. https://doi.org/10.1101/2021.04.13.439700

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