Biogenesis of C. elegans spermatogenesis small RNAs is initiated by a zc3h12a like ribonuclease

Small RNAs regulate spermatogenesis in many species, ranging from Caenorhabditis elegans to mammals. In C. elegans, two Argonaute proteins, ALG-3 and ALG-4, and their associated alg-3/4 26G-small RNAs are essential for spermatogenesis at 25°C and for imprinting paternal memory of germline gene expression in offspring. The alg-3/4 26G-small RNAs are antisense to their target mRNAs and are known to be produced by the RNA-dependent RNA polymerase, RRF-3. However, it remains unclear how the RNA templates for RRF-3 are generated and which cellular processes are affected by alg-3/4 26G-small RNAs. Here, we demonstrate a key role for the conserved zc3h12a-ribonuclease-like NYN-domain-containing protein, NYN-3, in spermatogenesis at 25°C. Expression of NYN-3 was temporally coordinated with ALG-3, and our sequencing of both total and 2xFLAG::ALG-3-immunoprecipitated small RNAs revealed that NYN-3 is required for the biogenesis of alg-3/4 26G small RNAs. We further used ePAR-CLIP sequencing to id...