[Bioinformatics] Today's Bioinformatics Seminar: Remo Rohs, Ph.D.

[Bioinformatics IDP-Seminar Series]

 "High-throughput Prediction of DNA Shape on a Genome-wide Scale"


Remo Rohs, Ph.D.
Molecular and Computational Biology Program, Departments of Biological Sciences and Chemistry, University of Southern California

TODAY, January 23, 2012
4:00pm
Gonda 1357
Abstract:
DNA sequence analysis views DNA as a linear string of letters. Yet, the nucleotides A, C, G, and T are chemical entities that give rise to the three-dimensional structure of DNA. The resulting shape of the double helix is sequence-dependent and plays a role in gene regulation. For example, the shape of the minor groove leads to specific variations in electrostatic potential, which in turn attract arginine residues. In addition, the strength of non-specific interactions in the nucleosome can also be regulated by DNA shape. Structural knowledge of DNA at atomic resolution derived from experimental studies is limited, and high-throughput sequencing technologies continue to provide a wealth of functional genomic sequences for which structural information is unavailable. To bridge this gap, we are developing a novel methodology for high-throughput prediction of DNA shape on a genome-wide basis. This approach has been used in a first application to analyze DNA shape of thousands of Hox protein binding sites, which resulted in new insights on how Hox genes have likely differentiated throughout evolution. In another application the DNA shape of thousands of unbound nucleosome binding sites indicates a periodicity of one helical turn even when the histone core is not present. DNA shape can now be predicted for whole genomes with the aim to integrate two areas of research that have developed along parallel lines, largely disconnected from each other: sequence and structure.

Host: Matteo Pellegrini, x50012



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