Intact RNA structurome reveals mRNA structure-mediated regulation of miRNA cleavage invivo.

Minglei Yang,Alberto Carbonell,Maria L Vigh,Jiawei Wang,Peter Brodersen,Yiliang Ding,Jitender Cheema,Qi Liu,Matthew Norris,Xiaofei Yang,Yueying Zhang,Hugh C Woolfenden,Xiaofeng Fang,Sha Yu

doi:10.1093/nar/gkaa577

Abstract

MicroRNA (miRNA)-mediated cleavage is involved in numerous essential cellular pathways. miRNAs recognize target RNAs via sequence complementarity. In addition to complementarity, in vitro and in silico studies have suggested that RNA structure may influence the accessibility of mRNAs to miRNA-induced silencing complexes (miRISCs), thereby affecting RNA silencing. However, the regulatory mechanism of mRNA structure in miRNA cleavage remains elusive. We investigated the role of in vivo RNA secondary structure in miRNA cleavage by developing the new CAP-STRUCTURE-seq method to capture the intact mRNA structurome in Arabidopsis thaliana. This approach revealed that miRNA target sites were not structurally accessible for miRISC binding prior to cleavage in vivo. Instead, we found that the unfolding of the target site structure plays a key role in miRISC activity in vivo. We found that the single-strandedness of the two nucleotides immediately downstream of the target site, named Target Adjacent nucleotide Motif, can promote miRNA cleavage but not miRNA binding, thus decoupling target site binding from cleavage. Our findings demonstrate that mRNA structure in vivo can modulate miRNA cleavage, providing evidence of mRNA structure-dependent regulation of biological processes.

Highlights

MicroRNAs (MiRNAs) are ∼21 nt RNAs that are involved in various aspects of development and stress responses by post-transcriptionally regulating gene expression [1]
MiRNAs are loaded onto ARGONAUTE proteins (AGO) to form functional post-transcriptional gene silencing effector complexes, miRNA-induced silencing complexes [2]. miRISC is guided by the miRNA to bind to target RNAs through sequence complementarity and to cleave the target RNAs [3,4]
By assessing the structure features flanking the miRNA target sites, we find that the single-strandedness of the two nucleotides immediately downstream of the target site, which we named Target Adjacent nucleotide Motif (TAM), can promote miRNA cleavage but not miRNA binding

Summary

Introduction

MicroRNAs (MiRNAs) are ∼21 nt RNAs that are involved in various aspects of development and stress responses by post-transcriptionally regulating gene expression [1]. Previous studies found that sequence complementarity is not the sole factor dictating miRNA cleavage [2], with RNA structure suggested to influence the silencing efficiency [5,6,7]. These studies were unable to reveal native RNA structure features for several reasons. The target site together with the flank regions were assessed as one, making it difficult to separate the contribution from each region [5,6,7] This confounded the identification of a specific RNA structure motif that regulated miRNA cleavage

Methods

Results

Conclusion