Endogenous transcripts direct microRNA degradation in Drosophila, and this targeted degradation is required for proper embryonic development

MicroRNAs (miRNAs) typically direct degradation of their mRNA targets. However, five miRNA targets in vertebrate animals are reported to have unusual miRNA-binding sites that direct degradation of cognate miRNAs. Here, we identify six sites, five in mRNAs and one in a non-coding RNA named Marge, that serve this purpose in Drosophila cells or embryos, which shows that target-directed miRNA degradation (TDMD) shapes endogenous miRNA levels in some invertebrate animals. The six sites direct miRNA degradation without collateral target degradation, helping to explain the potency of this miRNA-degradation pathway. Mutations that disrupt this pathway in Drosophila are lethal, with many flies dying as embryos. Derepression of miR-3 and its paralog miR-309 is responsible for some of this lethality, whereas the loss of Marge-directed degradation of miR-310 miRNAs causes defects in embryonic cuticle development. Thus, TDMD is strongly implicated in the viability of an animal and is required for its proper development. Samples analyzed from dora[A], dora[B], and CR43432 fly lines (each with paired wild-type controls), as well as from Drosophila S2 cells. At least two fly lines (or clonal S2 lines) serve as replicates for each dataset. For fly lines, mRNA and sRNA samples were collected at various timepoints throughout embryonic development.