Expression of small RNAs during epigenetic disturbances of Tetrahymena DNA elimination

Epigenetic inheritance of acquired traits is widespread among eukaryotes but how and to what extent such information is trans-generationally inherited is still unclear. The patterns of programmed DNA elimination in ciliates are epigenetically and trans-generationally inherited, and it has been proposed that small RNAs, which shuttle between the germline and the soma, regulate this epigenetic inheritance. In this study, we test the existence of such small RNA-mediated communication by epigenetically disturbing the pattern of DNA elimination in Tetrahymena. We show that the pattern of DNA elimination is indeed determined by the selective turnover of small RNAs, which is induced by the interaction between germline-derived small RNAs and the somatic genome. In addition, we show that DNA elimination of an element is regulated by small RNA-mediated communication with other eliminated elements. By contrast, no evidence obtained thus far supports the notion that transfer of epigenetic information from the soma to the germline, if any, regulates DNA elimination. Our results indicate that small RNA-mediated trans-nuclear and trans-element communication, in addition to unknown information in the germline genome, contributes to determining the pattern of DNA elimination. In this study, we aim to test the following three predictions regarding small RNA-directed DNA elimination in Tetrahymena by epigenetically disturbing DNA elimination: 1) selective turnover of Early-scnRNAs in scnRNA selection shapes the pattern of DNA elimination through communication between the MIC, the parental MAC and the developing new zygotic MAC; 2) trans-recognition between IESs via scnRNAs and the cis-spreading of Late-scnRNA production in the new MAC buffer against fluctuations in Early-scnRNA accumulation to ensure robust DNA elimination; and 3) IES-biased Early-scnRNA production in the MIC is determined at the end of the preceding conjugation by scnRNAs that translocate from the MAC to the new MIC.