Functional Diversification of Dicer-like Proteins and Small RNAs Required for Genome Sculpting

•scnRNAs in Paramecium are produced by cooperation of Dcl2 and Dcl3•scnRNAs are essential for complete epigenetic DNA and transposable element removal•A class of sRNAs produced by Dcl5—“iesRNAs”—precisely demarcates DNA ends•Both scnRNAs and iesRNAs are essential for complete DNA removal

SummaryIn eukaryotes, small RNAs (sRNAs) have key roles in development, gene expression regulation, and genome integrity maintenance. In ciliates, such as Paramecium, sRNAs form the heart of an epigenetic system that has evolved from core eukaryotic gene silencing components to selectively target DNA for deletion. In Paramecium, somatic genome development from the germline genome accurately eliminates the bulk of typically gene-interrupting, noncoding DNA. We have discovered an sRNA class (internal eliminated sequence [IES] sRNAs [iesRNAs]), arising later during Paramecium development, which originates from and precisely delineates germline DNA (IESs) and complements the initial sRNAs (“scan” RNAs [scnRNAs]) in targeting DNA for elimination. We show that whole-genome duplications have facilitated successive differentiations of Paramecium Dicer-like proteins, leading to cooperation between Dcl2 and Dcl3 to produce scnRNAs and to the production of iesRNAs by Dcl5. These innovations highlight the ability of sRNA systems to acquire capabilities, including those in genome development and integrity.