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TRANSCompel: a database on composite regulatory elements in eukaryotic genes.

Olga V Kel-Margoulis1, Alexander E Kel, Ingmar Reuter

  • 1BIOBASE GmbH, Halchtersche Strasse 33, D-38304 Wolfenbüttel, Germany. oke@biobase.de

Nucleic Acids Research
|December 26, 2001
PubMed
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The TRANScompel database details composite regulatory elements (CEs), which involve transcription factor interactions crucial for gene regulation. This resource aids in understanding gene function and promoter prediction.

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Gene regulation relies on complex interactions between transcription factors (TFs) and DNA.
  • Composite regulatory elements (CEs), featuring closely situated TF binding sites, are key functional units for combinatorial gene regulation.
  • Understanding TF-DNA and TF-TF interactions within CEs is vital for deciphering gene expression patterns.

Purpose of the Study:

  • To introduce the TRANScompel database, a resource cataloging known composite regulatory elements.
  • To highlight the utility of CE information for promoter and gene function prediction, and gene engineering.
  • To present the CATCH program for identifying potential CEs in DNA sequences.

Main Methods:

  • Database curation of known composite regulatory elements, including binding sites, transcription factors, and experimental evidence of cooperative action.

Related Experiment Videos

  • Development of the CATCH program (CompelPatternSearch) for computational identification of potential CEs.
  • Web accessibility of the TRANScompel database and CompelPatternSearch tool.

    • Main Results:

    • The TRANScompel database provides detailed information on individual CEs, their associated transcription factors, and binding sites.
    • Experimental evidence supporting the cooperative action of transcription factors within CEs is included.
    • The CATCH program offers a tool for discovering novel CEs within DNA sequences.

    Conclusions:

    • The TRANScompel database and associated tools (CATCH) are valuable resources for researchers studying gene regulation.
    • Information on composite regulatory elements significantly enhances promoter and gene function prediction.
    • This resource supports advancements in applied gene engineering by providing insights into combinatorial gene control.