The ZSWIM8 ubiquitin ligase mediates target-directed microRNA degradation [datatset 7]

MicroRNAs (miRNAs) associate with Argonaute (AGO) proteins to direct widespread post-transcriptional gene repression. Although association with AGO typically protects miRNAs from nucleases, extensive pairing to some unusual target RNAs can trigger miRNA degradation. Here we found that this target-directed miRNA degradation (TDMD) required the ZSWIM8 Cullin-RING E3 ubiquitin ligase. This and other findings suggested and supported a mechanistic model of TDMD in which target-directed proteolysis of AGO by the ubiquitin–proteasome pathway exposes the miRNA for degradation. Moreover, loss-of-function studies indicated that the ZSWIM8 Cullin-RING ligase accelerates degradation of numerous miRNAs in cells of mammals, flies, and nematodes, thereby specifying the half-lives of most short-lived miRNAs. These results elucidate the mechanism of TDMD and expand the inferred role of TDMD in shaping miRNA levels in bilaterian animals. Overall design: mRNA expression profiling by RNA sequencing of polyclonal mammalian cell lines expressing either Cas9 and one of three non-targeting control gRNAs, or KRAB-dCas9 and either a non-targeting control gRNA, a CYRANO-targeting gRNA, or one of two ZSWIM8-targeting gRNAs. This study consists of libraries generated from two to three biological replicates.