Conserved Pseudoknots in lncRNA MEG3 Are Essential for Stimulation of the p53 Pathway

Long non-coding RNAs (lncRNAs) are key regulatory molecules, but unlike with other RNAs, the direct link between their tertiary structure motifs and their function has proven elusive. Here we report structural and functional studies of human maternally expressed gene 3 (MEG3), a tumor suppressor lncRNA that modulates the p53 response. We found that, in an evolutionary conserved region of MEG3, two distal motifs interact by base complementarity to form alternative, mutually exclusive pseudoknot structures (“kissing loops”). Mutations that disrupt these interactions impair MEG3-dependent p53 stimulation in vivo and disrupt MEG3 folding in vitro. These findings provide mechanistic insights into regulation of the p53 pathway by MEG3 and reveal how conserved motifs of tertiary structure can regulate lncRNA biological function. [Display omitted] •LncRNA MEG3 is a tumor suppressor that stimulates the p53 pathway•The p53-stimulating core of MEG3 comprises of two conserved, structured domains•Two distal motifs in the MEG3 core form pseudoknot interactions (“kissing loops”)•Mutations in these pseudoknots disrupt MEG3 architecture and impair its function Uroda et al. identify the structural and functional core of the human lncRNA MEG3, revealing that point mutations designed to disrupt the MEG3 fold impair function. The work proves the importance of lncRNA tertiary structure motifs for selective and specific control of key cellular processes such as the p53 stress response.