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The Promoter Module Library

Regulatory units like promoters, enhancers or silencers contain functional modules many of which consist of at least two transcription factor binding sites in conserved order, separated by a spacer.

The Promoter Module Library is based on a compilation of such composite elements of two or more transcription factor binding sites. All of these promoter modules were shown to exhibit synergistic, antagonistic, or additive functions. References for the function and the experimental verification of the function are available for each promoter module.

The current Promoter Module Library (Version 5.1) consists of 670 regulatory modules (607 vertebrate modules and 63 plant modules).

ModelInspector is able to scan sequences for matches to the complete library or for selected promoter modules. All modules show a high specificity, revealing less than 1 match per 10,000 base pairs.

Example for a Promoter Module

The NF-kappa-B / IRF1 regulatory module is derived from one MHC class I HLA-B gene promoter. It mediates the synergistic induction of the HLA-B gene and other promoters by TNF and interferons.

Features of the NF-kappa-B / IRF1module:

• The module was derived from a single HLA-B promoter sequence.
• A database search with this module detects
  • all known promoter sequences of HLA-B genes
  • almost all HLA-A sequences which are regulated in the same synergistic way as HLA-B
  • one promoter of a beta-2-microglobulin gene which is coexpressed as a heterodimer with MHC class I antigens (the only one present in the primate section of GenBank Release 107)
  • five beta-interferon promoter sequences which are known to share the same synergistic activation with HLA-B genes
• These results cannot be obtained by database similarity searches like BLAST or FASTA.