Title: Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli
Authors: Meysman, Pieter ×
Dang, Thanh Hai
Laukens, Kris
De Smet, Riet
Wu, Yan
Marchal, Kathleen
Engelen, Kristof #
Issue Date: Jan-2011
Publisher: Oxford University Press
Series Title: Nucleic Acids Research vol:39 issue:2
Article number: e6
Abstract: Recognition of genomic binding sites by transcription factors can occur through base-specific recognition, or by recognition of variations within the structure of the DNA macromolecule. In this article, we investigate what information can be retrieved from local DNA structural properties that is relevant to transcription factor binding and that cannot be captured by the nucleotide sequence alone. More specifically, we explore the benefit of employing the structural characteristics of DNA to create binding-site models that encompass indirect recognition for the Escherichia coli model organism. We developed a novel methodology [Conditional Random fields of Smoothed Structural Data (CRoSSeD)], based on structural scales and conditional random fields to model and predict regulator binding sites. The value of relying on local structural-DNA properties is demonstrated by improved classifier performance on a large number of biological datasets, and by the detection of novel binding sites which could be validated by independent data sources, and which could not be identified using sequence data alone. We further show that the CRoSSeD-binding-site models can be related to the actual molecular mechanisms of the transcription factor DNA binding, and thus cannot only be used for prediction of novel sites, but might also give valuable insights into unknown binding mechanisms of transcription factors.
ISSN: 0305-1048
Publication status: published
KU Leuven publication type: IT
Appears in Collections:Centre of Microbial and Plant Genetics
Microbial and Molecular Systems - miscellaneous
× corresponding author
# (joint) last author

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