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

In Silico Biol. 2003;3(1-2):71-9. Epub 2002 Dec 8.

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-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).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Binding Sites
  • CCAAT-Enhancer-Binding Proteins / genetics*
  • CCAAT-Enhancer-Binding Proteins / metabolism
  • Consensus Sequence
  • DNA Primers
  • Epithelial Cells / microbiology
  • Epithelial Cells / physiology
  • Gene Expression Regulation
  • Genome, Human
  • Humans
  • NF-kappa B / genetics*
  • NF-kappa B / metabolism
  • Pseudomonas aeruginosa / pathogenicity
  • Pseudomonas aeruginosa / physiology*
  • Transcription, Genetic

Substances

  • CCAAT-Enhancer-Binding Proteins
  • DNA Primers
  • NF-kappa B