Past Event: Oden Institute Seminar

G-Dash: A genomics dashboard uniting physical and informatics studies of DNA, nucleosomes and chromatin

Thomas Bishop, Louisiana Tech University

Abstract

Historically, bioinformatics and computational biology are recognized as distinct endeavors. The underlying theories, experiments, software and computing resources differ significantly. We demonstrate that these differences can be overcome by exploiting existing data standards, algorithms, and web based tools to study the structure of DNA, nucleosomes and chromatin in atomic and coarse grain detail from single base pairs to megabase regions of chromatin and beyond. In this presentation I will define the “genomics dashboard” concept, explain the mathematics and algorithms that drive G-Dash , our prototype genome dashboard, then demonstrate how experimentally determined maps of nucleosome positions for Saccharomyces cerevisiae can be used to assemble a computational karyotype. Comparative all atom molecular dynamics simulations of nucleosomes and coarse-grained models of the MMTV, CHA1, HIS3 and PHO5 promoters highlight important observations. DNA kinking in the nucleosome depends on both sequence and position. Experimentally determined nucleosome positions are insufficient to achieve tight packing of chromatin. Sequence specific material properties of DNA (conformation & flexibility) can affect chromatin bending and looping.