RNAi-mediated regulation of alg-3 and alg-4 coordinates the spermatogenesis developmental program in C. elegans [small RNA-seq]
Developmental coordination of gene regulatory networks is necessary for maintaining fertility. Inappropriate activation or silencing of genes responsible for promoting the totipotent germ cell fate into oocytes and/or sperm can have detrimental effects on an organism's reproductive potential. Spermatogenesis and oogenesis are temporally separated within the germline tissue during the L4 and adult developmental stages, respectively. Yet, it remains unclear how these developmental programs are robustly executed, particularly during stressful conditions. Here we show evolutionarily conserved RNA interference (RNAi) pathways act to restrict expression of spermatogenesis genes to the L4 developmental stage during heat stress. We performed differential expression analysis of mRNA-seq and small RNA-seq libraries from L4 and adult-stage wild-type and mut-16 mutants, which lack a critical RNAi pathway protein, grown at permissive (20ºC) and elevated temperature (25ºC). Our analyses revealed spermatogenesis-enriched gene expression is developmentally mis-regulated in a small RNA-dependent manner at elevated temperature. Many of the mis-regulated spermatogenesis genes are targets of the ALG-3/4 pathway, which is critical for thermotolerant male fertility. We found that the genomic loci of alg-3 and alg-4 are targeted by small RNAs, and that during heat stress, MUT-16-dependent small RNAs are required for L4 stage-specific expression of the Argonautes, ALG-3 and ALG-4. These findings indicate that RNAi pathways are essential for properly coordinating the developmental program of spermatogenesis during heat stress. We propose that appropriate expression of spermatogenesis genes is achieved through small RNA-mediated genetic switches that regulate the expression of ALG-3 and ALG-4 to control ALG-3/4 pathway function throughout development. Moreover, this work provides key insights into the different molecular mechanisms that RNAi pathways employ to maintain both maternal and paternal germ cells' reproductive potential, and further highlights the complexities and importance of RNAi-mediated gene regulation in development. Overall design: 8 mRNA-seq and 8 small RNA-seq libraries were generated and analyzed. Each genotype per condition were generated in duplicate.