TRANSCompel®
The TRANSCompel® database is devoted to the particular aspect of gene transcriptional regulation [1-7]. It contains information about composite elements - the basic structures of combinatorial gene regulation [7]. Composite regulatory elements consist of two or three closely situated binding sites for distinct transcription factors (TFs), and represent minimal functional units providing combinatorial transcriptional regulation. Both specific factor-DNA and factor-factor interactions contribute to the function of composite elements. Each database entry corresponds to an individual composite element within a particular gene and contains information about two or three binding sites, the corresponding TFs, experiments confirming cooperative action between TFs. Interacting factors may differ by the structure of DNA-binding, activation, oligomerization and other domains. Along with structural differences, functional properties of TFs and hence their specific contribution to the transcription regulation may significantly vary. Co-operative action of the TFs within the composite elements results in a new highly specific pattern of gene transcription that cannot be provided by the involved factors separately. Composite elements are structural-functional units that provide cross-coupling of gene regulatory pathways and, in particular, cross-coupling of signal transduction pathways. There are two main types of composite elements: synergistic and antagonistic ones. In synergistic CEs, simultaneous interactions of two factors with closely situated target sites results in a non-additive high level of a transcriptional activation. Within an antagonistic CE two factors interfere with each other. Information about the structure of known composite elements and specific gene regulation achieved through such composite elements appears to be extremely useful for promoter prediction, for gene function prediction and for applied gene engineering as well. A program CATCH® for searching potential composite elements in DNA sequences has been developed. A sequence under study is scanned by this program using all composite elements collected in TRANSCompel® as individual searching patterns. Several parameters are available restricting the search: maximal mismatches in the cores of site1 and site2 comprising the composite elements, maximal variation of the distance between two sites, and composite score cut-off value. The composite score reflects how well the match coincides with the known examples of the composite elements in TRANSCompel®. This scoring function takes into account the number of mismatches in both sites and the distance between them. All found matches are directly linked to the TRANSCompel® entries containing the corresponding composite elements.
Webpage:
http://www.gene-regulation.com/pub/databases.html#transcompel
Tags:
nucleic acid sequence transcription
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