Biophysical Society Thematic Meeting| Santa Cruz 2018

Genome Biophysics: Integrating Genomics and Biophysics to Understand Structural and Functional Aspects of Genomes

Tuesday Speaker Abstracts

G-Dash: A Genomics Dashboard That Unites Physics and Informatics Studies of Chromatin

Thomas C. Bishop 1 ; Zilong Li 1 ; Ran Sun 1 ; 1 Louisiana Tech University, Physics, Ruston, Louisiana, United States

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. We define a genomics dashboard as a console that can track, analyze or display genomics information and that provides controllers or other means for manipulating chromatin structure. We present G-Dash as a prototype of the genomics dashboard concept. G-Dash unites our Interactive Chromatin Modeling(ICM) webserver’s capabilities with the Dalliance Genome Browser(DGB), utilizes a simple coarse grained model of chromatin implemented in LAMMPS for structure relaxation and displays 3D models with JSmol. All atom models of individual nucleosomes can also be generated. Thus, data obtained from public databases through the genome browser (e.g. experimentally or theoretically determined nucleosome positions) can be used to manipulate nucleosomes (add, delete and move), assign unique conformational states (e.g. tetrasome, octasome, chromatosome), display 3D structural data as tracks in the genome browser (e.g. Roll, Slide or Twist) or map informatics data onto a 3D structure (e.g. nucleosome positions, DNA damage sites, functional annotations). We demonstrate how experimentally determined maps of nucleosome positions for Saccharomyces cerevisiae can be used to assemble a computational karyotype. Models of the MMTV, CHA1, HIS3 and PHO5 promoters highlight important observations: experimentally determined nucleosome positions are insufficient to achieve tight packing of chromatin and sequence specific material properties of DNA (conformation and flexibility) can affect chromatin bending and looping. As a tool G-Dash supports cross-validation of physical modeling and informatics approaches and provides a means of investigating structure-function relationships for a genome. See the “Genome Dashboard” tab at http://dna.engr.latech.edu.

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