Intact RNA structurome reveals mRNA structure-mediated regulation of miRNA cleavage in vivo. Issue 15 (11th July 2020)

• Record Type: Journal Article
• Authors: Yang, Minglei; Woolfenden, Hugh C; Zhang, Yueying; Fang, Xiaofeng; Liu, Qi; Vigh, Maria L; Cheema, Jitender; Yang, Xiaofei; Norris, Matthew; Yu, Sha; Carbonell, Alberto; Brodersen, Peter; Wang, Jiawei; Ding, Yiliang
• Is Part Of: Nucleic acids research. Volume 48:Issue 15(2020)
• Page Start: 8767
• Page End: 8781
• Publication Date: 2020-07-11
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkaa577
• Languages: English
• ISSNs: 0305-1048

Abstract

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.