Formal grammar modeling three-stranded DNA:RNA braids

Mathematical Biology Seminar
Wednesday, April 13, 2022 - 10:00am for 1 hour (actually 50 minutes)
Margherita Maria Ferrari – University of South Florida – mmferrari@usf.edu
Bo Lin

Meeting Link: (Meeting ID: 948 8229 0086, Passcode: 264830)

Abstract: R-loops are three-stranded structures formed by a DNA:RNA hybrid and a single strand of DNA, often appearing during transcription. Although R-loops can threaten genome integrity, recent studies have shown that they also play regulatory roles in physiological processes. However, little is known about their structure and formation. In this talk, we introduce a model for R-loops based on formal grammars, that are systems to generate words widely applied in molecular biology. In this framework, R-loops are described as strings of symbols representing the braiding of the strands in the structure, where each symbol corresponds to a different state of the braided structure. We discuss approaches to develop a stochastic grammar for R-loop prediction using experimental data, as well as refinements of the model by incorporating the effect of DNA topology on R-loop formation.