Two classes of endogenous small RNAs in Tetrahymena thermophila

Abstract

Endogenous small RNAs function in RNA interference (RNAi) pathways to guide RNA cleavage, translational repression, or methylation of DNA or chromatin. In Tetrahymena thermophila, developmentally regulated DNA elimination is governed by an RNAi mechanism involving ∼27-30-nucleotide (nt) RNAs. Here we characterize the sequence features of the ∼27-30-nt RNAs and a ∼23-24-nt RNA class representing a second RNAi pathway. The ∼23-24-nt RNAs accumulate strain-specifically manner and map to the genome in clusters that are antisense to predicted genes. These findings reveal the existence of distinct endogenous RNAi pathways in the unicellular T. thermophila, a complexity previously demonstrated only in multicellular organisms. © 2006 by Cold Spring Harbor Laboratory Press.