Non-coding RNAs as genome sculptors

The conventional view of molecular biology dictates that the genetic information from DNA is translated, through RNA, into proteins. One of the major implications of this rule is that the observable phenotype of an organism is determined by the proteome, a notion that has been disproven by our growing knowledge about the emerging roles of non-coding RNAs. Using high throughput genomic and proteomic tools, I have probed the role of small and long non-coding RNAs in mediating programmed genome rearrangements in the ciliate, Oxytricha trifallax. Oxytricha, a member of stichotrich ciliates, displays a scrambled germline genome. The assembly of a functional somatic genome involves elimination of repetitive DNA elements including transposons, and reordering of gene fragments from the germline genome. Abrogation of non-coding RNA pathways leads to defects in chromatin architecture and DNA rearrangements, which begs the question whether similar mechanisms are involved in mediating gross chromosomal rearrangements in genomic disorders like cancer.