The developmentally timed decay of an essential microRNA family is seed-sequence dependent

MicroRNA (miRNA) abundance is tightly controlled by regulation of biogenesis and decay. Here, we show that the mir-35 miRNA family undergoes selective decay at the transition from embryonic to larval development in C. elegans. The seed sequence of the miRNA is necessary and largely sufficient for this regulation. Sequences outside the seed (3' end) regulate mir-35 abundance in the embryo but are not necessary for sharp decay at the transition to larval development. Enzymatic modifications of the miRNA 3' end are neither prevalent nor correlated with changes in decay, suggesting that miRNA 3' end display is not a core feature of this mechanism and further supporting a seed-driven decay model. Our findings demonstrate that seed-sequence-specific decay can selectively and coherently regulate all redundant members of a miRNA seed family, a class of mechanism that has great biological and therapeutic potential for dynamic regulation of a miRNA family's target repertoire. To test the role of miRISC-mediated slicing in invertebrates, we used CRISPR/Cas9-mediated genome editing to mutate the DEDH catalytic tetrad to AEDH in the major C. elegans microRNA Argonautes, ALG-1 and ALG-2 (alg-1(AEDH); alg-2(AEDH)). To determine the impact of mutating Argonautes’ catalytic residues on C. elegans microRNAs, we profiled small RNAs from embryos, L4 stage larvae and young adults. We also profiled small RNAs from embryos that were single mutants, with catalytic residues mutated in either ALG-1 or ALG-2. To test whether Target-directed microRNA degradation contributed to downregulation of select miRNAs in alg-1(AEDH); alg-2(AEDH), we added mutations to this background that theoretically inactivate all TDMD (ebax-1(null)) or TDMD of a mir-243 alone (Y47(mir-243bs_del)) and sequenced small RNAs in young adults.