Small RNA Mediated Genome Rearrangements in Oxytricha trifallax

Genomic rearrangements are prevalent in human DNA and are one of many reasons for the complexity of life. Oxytricha trifallax as ciliated protozoan contain macronuclei which are the somatic nuclei, and micronuclei which are the germline nuclei.  The macronucleus contains nanochromosomes coding for single genes. During mating, the micronuclei undergo meiosis that produce haploid micronuclei which are exchanged with a partner. The haploid micronuclei fuse to form a diploid micronucleus which divides by mitosis. One daughter micronuclei remain as a micronucleus, while the other undergoes a complex set of events to become a new macronucleus. Recently, it has been discovered that guide RNAs help transform large pieces of scrambled micronuclear DNA into small, functional macronuclear DNA genes. We identified potential guide RNAs from mating ciliates and where they originate. This was done by isolating RNA during large matings by lysing the cells and constructing a library for high throughput sequencing. By comparing the sequence to both the macronuclear and micronuclear genome, we found 27 nucleotide RNAs (27mac RNA) that map to specific regions of the nanochromosomes in parental macronuclei and are transcribed from both strands. The 27mac RNAs appear at 24 hours after mixing the two strains and gradually disappear. Peering into the processes of macronuclear development in these ciliates can provide clues to the mechanisms guiding genome regulation. Understanding the way in which the 5% of micronuclear DNA that ends up in the macronucleus is identified and processed will lead to a better understanding of how eukaryotes rearrange genomes.