Prediction of potential C/EBP/NF-kappaB composite elements using matrix-based search methods.

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-kappaB plays a central role, but its effects have to be specified by cooperation with additional factors. NF-B 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 previously existing C/EBP matrices, established a model for C/EBP/ NF-kappaB 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).