Otiwi1-interacting RNAs at four time points during Oxytricha conjugation

Genome duality in ciliated protozoa offers a unique system to showcase their epigenome as a model of inheritance. In Oxytricha, the somatic genome is responsible for vegetative growth, while the germline contributes DNA to the next sexual generation. Somatic nuclear development eliminates all transposons and other "junk DNA", which constitute ~95% of the germline. We demonstrate that Piwi-interacting small RNAs (piRNAs) from the maternal nucleus can specify genomic regions for retention in this process. Oxytricha piRNAs map primarily to the somatic genome, representing the ~5% of the germline that is retained. Furthermore, injection of synthetic piRNAs corresponding to normally-deleted regions leads to their retention in subsequent generations. Our findings highlight small RNAs as powerful transgenerational carriers of epigenetic information for genome programming. Overall design: We sequenced sRNAs enriched by Otiwi1 co-IP at 12, 19, 23 and 30 hr post-mixing during Oxytricha sexual development. RNA ChIP with Otiwi1 antibody (Abcam, cat# ab12337, lot#868987) enriched 27nt sRNAs in Oxytricha at 12, 19, 23 and 30 hr post-mixing of mating types.