Nucleus-Independent Transgenerational Small RNA Inheritance in Caenorhabditis elegans
In C. elegans worms, epigenetic information transmits transgenerationally. Still, it is unknown whether the effects transfer to the next generation inside or outside of the nucleus. Here we use the tractability of gene-specific double-stranded RNA-induced silencing to demonstrate that RNAi can be inherited independently of any nuclear factors via mothers that are genetically engineered to transmit only their ooplasm but not the oocytes' nuclei to the next generation. We characterize the mechanisms and, utilizing RNA sequencing, chimeric worms and sequence polymorphism between different isolates, identify endogenous small RNAs which, similarly to exogenous siRNAs, are inherited in a nucleus-independent manner. From an historical perspective, these results might be regarded as partial vindication of discredited cytoplasmic inheritance theories from the 19th century, such as Darwin's “pangenesis” theory. Overall design: RNA was extracted from "day one" adult nematodes of different isolates (N2 and MY16). The samples include 3 biological replicates of worms in four  conditions (MY16, MY16_star, N2, N2_star). 11 samples are from small RNA sequencing (one sample from MY16_star failed to yield sufficient RNA) and 12 samples are from total RNA sequencing, yielding a total of 23 samples.