A lncRNA drives developmentally timed decay of all members of an essential microRNA family

The spatiotemporal expression patterns of microRNAs (miRNAs) are crucial to their function. Target-directed miRNA degradation (TDMD) is an emerging regulatory module that contributes to these expression patterns wherein a specialized RNA (a TDMD trigger) drives miRNA decay through base pairing and the resulting recruitment of E3 ubiquitin ligase ZSWIM8/EBAX-1. Extensive base pairing to the miRNA seed region and 3' end has been proposed as a key feature that distinguishes TDMD triggers from conventional mRNA targets of miRNAs, which primarily pair with the seed. Here we identify the long noncoding RNA tts-2 as a TDMD trigger for mir-35-42, the most abundant miRNA family in Caenorhabditis elegans early embryos. We demonstrate that a single site in tts-2 drives decay through base pairing with the seed sequence shared by all eight family members. A second site in tts-2 supports decay of mir-38 with incomplete seed complementarity. Retargeting tts-2 to other miRNAs suggests that the GC-rich seed of mir-35-42 allows for seed-sufficient TDMD. Our findings demonstrate that extended base pairing is not a universal requirement of TDMD and that TDMD drives developmentally timed clearance of abundant miRNAs at the exit of C. elegans embryogenesis.