An antisense noncoding RNA enhances translation via localized structural rearrangements of its cognate mRNA

Abstract A large portion of eukaryotic genes are associated with noncoding, natural antisense transcripts (NATs). Despite sharing extensive sequence complementarity their sense mRNAs, mRNA–NAT pairs elusively often evade dsRNA-cleavage and siRNA-triggered silencing. More surprisingly, some NATs enhance translation mRNAs by yet unknown mechanism(s). Here, we show that enhancement the rice (Oryza sativa) PHOSPHATE1.2 (PHO1.2) mRNA is enabled specific structural rearrangements guided its noncoding RNA (cis-NATpho1.2). Their interaction in vitro revealed no evidence widespread intermolecular dsRNA formation, but rather local changes nucleotide base pairing, leading to higher flexibility PHO1.2 at a key high guanine-cytosine?(GC) regulatory region inhibiting translation, ?350-nt downstream start codon. Sense–antisense increased formation 80S complex PHO1.2, possibly inducing rearrangement within this inhibitory region, thus making more accessible 60S. This work presents framework for resolution studies functional mRNA–antisense pairs.