An endogenous cluster of target-directed microRNA degradation sites induces decay of distinct microRNA families

While much is known about microRNA (miRNA) biogenesis and targeting, relatively less is understood about miRNA decay. Target-directed miRNA degradation (TDMD) is a mechanism in metazoans where certain RNAs can "trigger" miRNA decay. All known TDMD triggers base pair with the miRNA seed, and extensively base pair on the miRNA 3' end, a pattern that is believed to be a requirement for miRNA turnover. Using Ago1-CLASH, we find that the Drosophila transcript Kah contains at least two triggers, a "trigger cluster," against miR-9b and the miR-279 family. One trigger contains minimal/non-canonical 3' end base-pairing but is still sufficient to induce TDMD of the miR-279 family. We find that these clustered triggers lack cooperativity, that minimal 3' pairing is required for miR-279 family turnover, and probed the in-cell structure of the Kah trigger cluster. Overall, we expand the list of endogenous TDMD triggers, which revealed unexpectedly complex regulation in miRNA turnover.