A conserved RNA regulates miRNA turnover and animal behavior through a near-perfect miRNA site

Metazoan high complementarity microRNA (miRNA) binding sites can induce miRNA turnover through 3' tailing and trimming, however the in vivo importance of this mechanism remains unknown. Here, we show that a transcript harboring a highly complementary and deeply conserved miRNA binding site for miR-29 controls zebrafish and mouse behavior. This brain-enriched transcript originated in distal vertebrates as a long noncoding RNA, which we called libra (lncRNA involved in behavioral alterations), and evolved to the protein-coding gene known as NREP in mammals where the miR-29 binding site is located within the 3'UTR. libra-deficiency results in viable fish that manifest abnormal exploration behavior. To determine if the Nrep transcript retained the regulatory noncoding function and to define the contribution of the highly complementary miR-29 binding site, we generated the NrepmiR-29scr allele in mice where the sequence of the site was scrambled to specifically uncouple Nrep function from miR-29 regulation. We show that the Nrep miR-29 binding site restricts miR-29b expression in the cerebellum. The ectopic miR-29b expression in NrepmiR-29scr mice is associated with altered cerebellum function and behavior. We finally show that the near-perfect miRNA site triggers miR-29b turnover through 3' trimming. In summary, we demonstrate the first example of an endogenous RNA-directed miRNA degradation event in vivo that is required for normal animal behavior. Overall design: Total RNA profiles of 72hpf embryos of zebrafish wild type (wt), full deletion of libra locus (libradel) and inversion of the libra conserved region (librainv) in technical duplicate; Size-selected small RNA profiles of wild type and NrepmiR-29scr mouse NPCs (n=3 for both lines)

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Bitetti A, Mallory AC, Golini E, Carrieri C, Carreño Gutiérrez H, Perlas E, Pérez-Rico YA, Tocchini-Valentini GP, Enright AJ, Norton WHJ, Mandillo S, O'Carroll D, Shkumatava A