Prediction of Potential C/EBP/NF-κB Composite Elements Using Matrix-Based Search Methods

Issue title: 3rd International Conference on Bioinformatics of Genome Regulation and Structure (BGRS 2002), June 2002, Novosibirsk, Russia

Article type: Research Article

Authors: Shelest, Ekaterina^; | Kel, Alexander | Gößling, Ellen | Wingender, Edgar^;

Affiliations: GBF German Research Centre for Biotechnology, Mascheroder Weg 1, D-38124 Braunschweig, Germany, E-mail: ksl@gbf.de | BIOBASE GmbH, Halchtersche Str. 33, D-38304 Wolfenb¨ttel, Germany | Permanent address: Institute of Cytology and Genetics SB RAN, Lavrentyev pr., 10, 630090, Novosibirsk, Russia

Note: [] Corresponding author

Abstract: Bacterial infections trigger a wide range of host cell responses. For the interaction of Pseudomonas aeruginosa and epithelial cells it is known that transcription factor NF-κB plays a central role, but its effects have to be specified by cooperation with additional factors. NF-κB containing composite elements, e.g. with C/EBP, may be appropriate indicators for new antibacterial response genes. We refined matrix-based search methods for C/EBP, which was necessary because of weak consensi of the previosly existing C/EBP matrices, established a model for C/EBP / NF-κB composite element, used it for scanning all known human 5'-flanking sequences and identified 135 new candidate genes. The newly constructed C/EBP binding patterns will be available with one of the next releases of the TRANSFAC database (http://www.gene-regulation.de).

Keywords: promoters, regulatory sequence signals, transcription factors, transcription factor binding sites, composite elements, antibacterial response

Journal: In Silico Biology, vol. 3, no. 1,2, pp. 71-79, 2003