Speaker: Nataša Jonoska, Ph.D.
Professor of Mathematics, University of South Florida
Title: RNA guided DNA rearrangements and RNA-DNA hybrids
We concentrate on two non-standard roles of transcript RNA: RNA templated DNA recombination and formation of co-transcriptional RNA-DNA hybrids also known as R-loops. — RNA has been observed as a template for DNA recombinant processes during development of somatic nuclei in some species of ciliates. We show DNA recombination models based on 4-regular graphs and Gauss codes. We illustrate these models in a well studied ciliate species Oxytricha trifallax where DNA rearrangement is observed on a massive scale. — R-loops are transient three-stranded nucleic acids that form during transcription when the nascent RNA hybridizes to the template DNA, freeing the DNA coding strand. These structures may play important roles in physiological processes such as control of gene expression, while also contributing to chromosomal instability and disease. We show a formal grammar model approach to modeling R-loops. Although the model has no explicit topological information, the R-loop grammar seems to predict R-loop formation on plasmids with varying starting topologies.