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Ciliated protozoans possess two types of nuclei; a transcriptionally silent micronucleus, which serves as the germ line nucleus, and a transcriptionally active macronucleus, which serves as the somatic nucleus. The macronucleus is derived from a new diploid micronucleus after mating, with epigenetic information contributed by the parental macronucleus serving to guide the formation of the new macronucleus. In the stichotrichous ciliate  Oxytricha trifallax , the macronuclear DNA is highly processed to yield gene-sized nanochromosomes with telomeres at each end. Here we report that soon after mating of  Oxytricha trifallax , abundant 27 nt small RNAs are produced that are not present prior to mating. We performed next generation sequencing of  Oxytricha  small RNAs from vegetative and mating cells. Using sequence comparisons between macronuclear and micronuclear versions of genes, we found that the 27 nt RNA class derives from the parental macronucleus, not the developing macronucleus. These small RNAs are produced equally from both strands of macronuclear nanochromosomes, but in a highly non-uniform distribution along the length of the nanochromosome, and with a particular depletion in the 30 nt telomere-proximal positions. This production of small RNAs from the parental macronucleus during macronuclear development stands in contrast to the mechanism of epigenetic control in the distantly related ciliate  Tetrahymena . In that species, 28–29 nt scanRNAs are produced from the micronucleus and these micronuclear-derived RNAs serve as epigenetic controllers of macronuclear development. Unlike the  Tetrahymena  scanRNAs, the  Oxytricha  macronuclear-derived 27 mers are not modified by 2′O-methylation at their 3′ ends. We propose models for the role of these “27macRNAs” in macronuclear development.

Mating of the Stichotrichous Ciliate Oxytricha trifallax Induces Production of a Class of 27 nt Small RNAs Derived from the Parental Macronucleus