UNIVERSITY OF MALTA
LIFE SCIENCE RESEARCH SEMINARS
Web: http://www.um.edu.mt/events/scisem/
Email: scisem@um.edu.mt
Abstract form
Title: Use of structural DNA properties for the prediction of regulatory
binding sites
Presenter: Pieter Meysman
Contact address: Arenbergpark 20, 3001 Leuven, Belgium
Tel: +32 16 329686
Fax:
Email: pieter.meysman@biw.kuleuven.be
Presentation date: 9th May 2011
Abstract
Molecular recognition of genomic target sites by transcription factors (TF) is a vital
process in the transcription regulation of genes. The types of physical interaction
that contribute to the recognition of TF binding sites can be roughly divided into
those enabling direct read-out and those that allow for indirect read-out. Direct readout comprises base-specific recognition, such as stabilizing hydrogen bonds
between amino acids of the TF protein and base pairs of the DNA molecule. Indirect
read-out refers to the usage of variations in the DNA structure itself as the basis for
recognition.
The direct form of recognition is the focus of most current endeavours to model TF
binding sites, usually by modelling a conserved set of nucleotides, e.g. a position
weight matrix or a consensus sequence. However by considering only a single
recognition mechanism, these approaches potentially overlook any information
concerning binding site identity contained within the structural DNA properties.
Therefore our goal was to create a binding site model that can also account for the
indirect read-out mechanisms of protein-DNA interaction. We were able to show that
by explicitly considering the structural properties of the DNA molecule, we could
improve the prediction of TF binding sites. Furthermore we confirmed that the
structural properties selected by our model are biologically relevant and thus this
approach can be used to provide insight into the binding mechanisms of
transcription factors.