[Bioinformatics] Today's Bioinformatics Seminar: Remo Rohs, Ph.D.
Bioinformatics IDP-Seminar Series
bioinformatics at lists.ucla.edu
Mon Jan 23 08:51:26 PST 2012
"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
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
IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the Bioinformatics