(1) Institute of Cytology and Genetics, Novosibirsk, Russia
(2) Gesellschaft fìr Biotechnologische Forschung
mbH, Maschroder Weg 1., D-38124 Braunschweig, Germany
http://transfac.gbf-braunschweig.de
kel@benpc.bionet.nsk.su;
ewi@venus.gbf-braunschweig.d400.de
http://transfac.gbf-braunschweig.de
The database on transcription regulatory regions in eukaryotic genomes (TRRD) have been developed [1] (http://www.bionet.nsk.su/TRRD.html; ftp://benpc.bionet.nsk.su/pub/trrd/). The main principle of data representation in TRRD is modular structure and hierarchy of transcription regulatory regions. TRRD entry corresponds to a gene as entire unit. Information on gene regulation is provided (cell-cycle and cell type specificity, developmental stage-specificity, influence of various molecular signals on gene expression). TRRD database contains information about structural organization of gene transcription regulatory region. TRRD contains description of known promoters and enhancers in 5', 3' regions and in introns. Description of binding sites for transcription factors includes nucleotide sequence and precise location, name of factors that bind to the site, experimental evidences for the binding site revealing. We provide cross-references to TRANSFAC database [2] for both sites and factors as well as for genes. TRRD 3.3 release includes 340 vertebrate genes. COMPEL database contains information about composite elements which are functional units essential for highly specific transcription regulation [3]. Direct interactions between transcription factors binding to their target sites within composite elements result in convergence of different signal transduction pathways. Nucleotide sequences and positions of composite elements, binding factors and types of their DNA binding domains, experimental evidence confirming synergistic or antagonistic action of factors are registered in COMPEL. Cross-references to TRANSFAC factors table are given. TRRD and COMPEL are provided by cross-references to each other. COMPEL 2.1 release includes 140 composite elements. We have developed a software for analysis of transcription regulatory region structure. The CompSearch program is based on oligonucleotide weight matrix method. To collect sets of binding sites for the matrixes construction we have used TRANSFAC and TRRD databases. The CompSearch program take into account the fine structure of experimentally confirmed NFATp/AP-1 composite elements collected in COMPEL (distances between binding sites in composite elements, their mutual orientation). By means of the program we have found potential composite elements of NFATp/AP- 1 type in the regulatory regions of various cytokine genes. Analysis of composite elements could be the first approach to reveal specific patterns of transcription signals encoding regulatory potential of eukaryotic promoters.
1. Kel O.V., Romachenko A.G., Kel A.E., Naumochkin A.N., Kolchanov
N.A. Proceedings of the 28th Annual Hawaii International Conference on
System Scienses [HICSS]. (1995), v.5, Biotechnology Computing, IEE
Computer Society Press, Los Alamos, California, p.42 -51
2.Wingender E., Dietze P., Karas H., and Knuppel R. TRANSFAC: a
database on transcription factors and their DNA binding sites (1996).
Nucl. Acids Res., 1996, v.24, pp. 238-241.
3.Kel O.V., A.G.Romaschenko, A.E.Kel, E.Wingender, N.A.Kolchanov.
A compilation of composite regulatory elements affecting gene
transcription in vertebrates (1995). Nucl. Acids Res., v.23,
pp.4097-4103.