The SPN-4 Rbfox RNA-binding protein selects maternal mRNAs for CCR4-NOT-dependent clearance in C. elegans embryos

The elimination of many maternal mRNAs is an essential feature of the maternal-to-zygotic transition. We report an essential pathway that clears many maternal transcripts from early C. elegans embryos using the RbFox-related SPN-4 RNA-binding protein as a specificity factor and the CCR4-NOT deadenylase complex as an effector. We biochemically identified SPN-4-associated mRNAs from late-stage oocytes and found that the set of SPN-4-associated transcripts is enriched for maternal mRNAs that undergo early decay. Single-molecule fluorescence in situ hybridization experiments established that many SPN-4-associated mRNAs fail to be eliminated in the absence of SPN-4. In the 3'UTRs of two target mRNAs, we identified RbFox motifs that bind SPN-4 in vitro and are required for SPN-4-dependent clearance in vivo. In a genetic screen to identify factors that work with SPN-4, we isolated alleles of CCR4-NOT components. Auxin-induced degradation of the LET-711/NOT1 scaffold and the CCF-1 deadenylase disrupted clearance of two SPN-4-associated transcripts. Our results support a model in which SPN-4 initiates expression in late-stage oocytes, associates with maternal mRNA targets through RNA sequences in their 3'UTRs and promotes CCR4-NOT-mediated decay during early embryogenesis. Overall design: Transcripts present in cell lysates and immunoprecipitates from SPN-4, LIN-41, and OMA-1 ribonuclear protein complexes were profiled by RNA sequencing. An amplification method was utilized for low input RNA because of the restricted distribution of SPN-4 in the adult C. elegans gonad.