The ZSWIM8 ubiquitin ligase mediates target-directed microRNA degradation [dataset 1]

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: miRNA expression profiling by small-RNA sequencing of K562 cells expressing inducible KRAB-dCas9 and either a control guide RNA (gRNA), a gRNA targeting CYRANO, or one of two gRNAs targeting ZSWIM8. This study consists of 12 libraries generated from three biological replicates per gRNA.