Argonaute-associated short introns are a novel class of gene regulators.. Agotron RIPseq

MicroRNAs (miRNAs) are short (~22 nucleotides) but important regulators of gene expression acting by direct base pairing to 3’UTR target sites in mRNAs. miRNAs are produced by two sequential endonucleolytic cleavages facilitated by Drosha in the nucleus and Dicer in the cytoplasm. A subclass of miRNAs, termed mirtrons, derives from short introns that bypass Drosha cleavage and instead enter the miRNA biogenesis pathway as Dicer substrates. In both cases, the dicer-cleaved RNA associates with Argonaute (Ago) proteins to mediate sequence-specific post-transcriptional gene silencing. Here we uncover a third biogenesis strategy that, similar to mirtron biogenesis, initiates from short introns but bypasses Dicer cleavage. These short introns (80-100 nucleotides), coined agotrons, are associated with and stabilized by Ago in the cytoplasm. In some cases, the intron is completely conserved in mammalian species, suggesting that they are functionally important. Importantly, we demonstrate that the agotrons are capable of repressing mRNAs with seed-matching target sequences in the 3’UTR. These data provide evidence for a novel type of miRNA-like regulator of gene-expression, which bypasses the canonical miRNA biogenesis machinery.