Intact RNA structurome reveals mRNA structure-mediated regulation of miRNA cleavage in vivo
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Intact RNA structurome reveals mRNA structure-mediated regulation of miRNA cleavage in vivo. / 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.
In: Nucleic Acids Research, Vol. 48, No. 15, 2020, p. 8767-8781.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Intact RNA structurome reveals mRNA structure-mediated regulation of miRNA cleavage in vivo
AU - Yang, Minglei
AU - Woolfenden, Hugh C.
AU - Zhang, Yueying
AU - Fang, Xiaofeng
AU - Liu, Qi
AU - Vigh, Maria L.
AU - Cheema, Jitender
AU - Yang, Xiaofei
AU - Norris, Matthew
AU - Yu, Sha
AU - Carbonell, Alberto
AU - Brodersen, Peter
AU - Wang, Jiawei
AU - Ding, Yiliang
PY - 2020
Y1 - 2020
N2 - 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.
AB - 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.
U2 - 10.1093/nar/gkaa577
DO - 10.1093/nar/gkaa577
M3 - Journal article
C2 - 32652041
AN - SCOPUS:85090491093
VL - 48
SP - 8767
EP - 8781
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - 15
ER -
ID: 249862406