Target RNA Secondary Structure Is a Major Determinant of miR159 Efficacy

Plant Physiology
Zihui ZhengAnthony A Millar

Abstract

In plants, microRNA (miRNA)-target complementarity has long been considered the predominant factor determining the silencing outcome of the miRNA-target interaction, although the efficacy of such interactions have rarely been appraised in plants. Here, we perform in planta silencing efficacy assays on seven Arabidopsis MYB genes, all of which contain conserved miR159-binding sites of analogous complementarity. These genes were found to be differentially silenced by miR159; MYB81, MYB97, MYB101, MYB104, and DUO1 were all poorly silenced, whereas MYB33 and MYB65 were strongly silenced. Curiously, this is consistent with previous genetic analysis defining MYB33 and MYB65 as the major functional targets of miR159. Neither the free energy of miR159-target complementarity, nor miRNA binding site accessibility, as determined by flanking region AU content, could fully explain the discrepancy of miR159 silencing efficacy. Instead, we found that MYB33 and MYB65 were both predicted to contain a distinctive RNA secondary structure abutting the miR159 binding site. The structure is composed of two stem-loops (SLs) that are predicted to form in MYB33/65 homologs of species as evolutionary distant as gymnosperms. Functional analysis found tha...Continue Reading

Citations

May 10, 2019·RNA Biology·Tao Ju Cui, Chirlmin Joo
Aug 28, 2020·Plant & Cell Physiology·Sha Yu, Jia-Wei Wang
Sep 28, 2018·Plant Methods·Umidjon ShapulatovAlexander R van der Krol
Aug 16, 2018·Nature Reviews. Molecular Cell Biology·Luca F R Gebert, Ian J MacRae
Aug 2, 2019·Plants·Anthony A MillarGigi Wong
Jul 5, 2019·Plants·María José López-GalianoCarolina Rausell
Dec 4, 2020·Genomics·Marcelino Martínez NúñezFlor de Fátima Rosas Cárdenas
Mar 5, 2021·Methods : a Companion to Methods in Enzymology·Veronica F Busa, Anthony K L Leung

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