Genome rearrangement is a driving force for evolution. Previous molecular studies on this subject have focused on DNA or chromatin transaction per se, or on protein machineries involved in DNA recombination and repair. Much less is known about the roles of RNA in genome rearrangement. Recent progresses on the studies of non-coding transcripts, on the other hand, have clearly demonstrated an expanding catalog of functional RNAs that regulate genes and genomes, encouraging the search for more ways in which RNA can shape the genome.;My thesis first utilizes the programmed genome remodeling in the ciliate Oxytricha as a model system to understand how a class of small RNAs called piRNAs facilitates genome-wide rearrangements. Through a combination of molecular, high-throughput sequencing, and synthetic biology approaches, I provide evidence for a model where piRNAs protect DNA against loss during Oxytricha genome rearrangement. This not only reveals a novel function for piRNAs, but also underscores a plasticity of RNA-based regulatory systems, because in two distantly-related ciliate species, small RNAs target DNA for deletion instead during genome reduction.;Genome rearrangement and instability is also a hallmark of cancer. Could RNA impact genome rearrangement during the evolution of cancer? In light of a previous study from our lab demonstrating RNA-templated DNA rearrangements in Oxytricha (Nowacki et al., 2008), I searched for chimeric transcripts in normal human cells to address the hypothesis that such chimeric RNAs may occasionally guide DNA rearrangements during tumorigenesis. By both computational and experimental analyses, I showed that even normal human cells produce chimeric RNAs, likely via RNA trans-splicing without corresponding DNA rearrangement. The fact that rearrangements at the level of RNA can precede that of DNA suggests the possibility that the presence of chimeric RNA may predispose the DNA genome to rearrangements.
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