The ZSWIM8 ubiquitin ligase mediates target-directed microRNA degradation [dataset3]

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 clonal K562 or Drosophila S2 cell lines that are either wild-type or knockout for ZSWIM8 (zswim8/Dora). Clonal lines were generated by single-cell sorting of parental lines transiently transfected with Cas9 and either a gRNA targeting ZSWIM8 (zswim8/Dora) or a non-targeting control gRNA. This study consists of libraries generated from three clonal lines per genotype for each of the two cell types.