Biophysical Society Thematic Meeting| Santa Cruz 2018

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

Monday Speaker Abstracts

Contributions of DNA Sequence in 3D Genomic Architectures Wilma K. Olson 1 Rutgers, the State University of New Jersey, Chemistry and Chemical Biology, Piscataway, New Jersey, United States One of the critical unanswered questions in genome biophysics is how the primary sequence of DNA bases influences the global properties of very long chain molecules. The local sequence- dependent features of DNA found in high-resolution structures introduce irregularities in the disposition of adjacent residues that facilitate the specific binding of proteins and modulate the global folding and interactions of the double helix. The contributions of DNA sequence reveal themselves in reduced molecular representations whereby the orientation and displacement of paired bases or successive base pairs are described in terms of a set of rigid-body parameters. The importance of this treatment lies in its utility in linking atomic observables with macromolecular properties, and in bridging the gap between the size of systems that can be studied at full atomic detail with events, such as protein-mediated looping, that take place at the mesoscale level. The local sequence also contributes to the positions of nucleosomes on DNA and the properties of the interspersed DNA linkers. Like the patterns of base-pair association within DNA, the arrangements of nucleosomes in chromatin modulate the properties of longer polymers. The spatial arrangements of interacting nucleosomes along short, well-defined arrays provide a basis for linking the mesoscale features of chromatin to higher-order structures. A nucleosome-level depiction of chromatin reduces the complexity of the system along the same lines as a base-pair level depiction of DNA and makes it possible to bridge the gap between chromatin ‘secondary structures’ and even longer polymers.

Modeling Gene Elements at Nucleosome Resolution

Tamar Schlick New York University, USA

No Abstract

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