Auto-regulation of miRNA biogenesis by let-7 and Argonaute

MicroRNAs (miRNAs) comprise a large family of small RNA molecules that post-transcriptionally regulate gene expression in many biological pathways(1). Most miRNAs are derived from long primary transcripts that undergo processing by Drosha to produce ~65 nucleotide (nt) precursors that are then cleaved by Dicer, resulting in the mature 22 nt forms(2,3). Serving as guides in Argonaute protein complexes, mature miRNAs use imperfect base-pairing to recognize sequences in mRNA transcripts, leading to translational repression and destabilization of the target mRNAs(4,5). Here we show that the miRNA complex also targets and regulates non-coding RNAs (ncRNAs) that serve as substrates for the miRNA processing pathway. We found that the C. elegans Argonaute, ALG-1, binds to a specific site at the 3′ end of let-7 miRNA primary transcripts and promotes downstream processing events. This interaction is mediated by mature let-7 miRNA via a conserved complementary site in its own primary transcript, thus creating a positive feedback loop. We further show that ALG-1 associates with let-7 primary transcripts in nuclear fractions. Argonaute also binds let-7 primary transcripts in human cells, demonstrating that the miRNA pathway targets non-coding RNAs in addition to protein-coding mRNAs across species. Moreover, our studies in C. elegans reveal a novel role for Argonaute in promoting biogenesis of a targeted transcript, expanding the functions of the miRNA pathway in gene regulation. This discovery of auto-regulation of let-7 biogenesis sets a new paradigm for controlling miRNA expression.