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TRANSCompel®


NAR Molecular Biology Database Collection entry number 345
Kel-Margoulis, O.1, Kel, A.1, Reuter, I.1, Deineko, I.2, Wingender, E.1
1BIOBASE GmbH, Halchtersche Strasse 33, D-38304 WolfenbÜttel, Germany
2Institute of Cytology & Genetics SB RAN, 10 Lavrentyev pr., 630090, Novosibirsk, Russia
Contact oke@biobase.de

Database Description

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.

Recent Developments

TRANScompel® 7.0 Public consists of two interlinked tables. The COMPEL table contains general information about the composite elements including sequence, positions, gene, names of cooperating transcription factors as well as a brief list of the experimental evidence. The EVIDENCE table provides detailed information about the experimental evidence confirming physical and functional interactions between the corresponding transcription factors. Genes and transcription factors are linked to the corresponding entries in the TRANSFAC® database [8]. TRANSCompel® 7.0 Public contains information about 322 composite regulatory elements. This version of TRANSCompel® equipped with the search and browse tools is available at http://www.gene-regulation.com/pub/databases.html#transcompel. The professional releases of TRANSCompel®, equipped by the CATCH® program, are available at Biobase GmbH (www.biobase-international.com; info@biobase.de).

Acknowledgements

The authors are grateful to Romaschenko A.G. and Kolchanov N.A. for valuable discussions on the concept of composite regulatory elements. Part of this work has been funded by grants of the German Ministry of Education and Research (BMBF) "Intergenomics" (031U210B), by European Commission under FP6 "Life sciences, genomics and biotechnology for health" contract LSHG-CT-2004-503568 "COMBIO".

References

1. Kel-Margoulis,O., Matys,V., Choi,C., Reuter,I., Krull,M., Potapov,A.P., Voss,N., Liebich,I., Kel,A., and Wingender,E. (2005) Databases on Gene Regulation. In Bajic,V.B. and Tan,T.W. (ed.), Information Processing And Living Systems. World Scientific Publishing Co, Singapore, Vol. 2, pp. 709-727.
2. Kel-Margoulis O., Kel A.E., Reuter I., Igor V. Deineko and Wingender E. (2002) TRANSCompel - a database on composite regulatory elements in eukaryotic genes. Nucleic Acids Res., 30, 332-334.
[3] Kel-Margoulis,O.V., Romaschenko,A.G., Kolchanov,N.A., Wingender,E., and Kel,A.E. (2000) COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation. Nucleic Acids Res., 28, 311-315.
3. Heinemeyer,T., Wingender,E., Reuter,I., Hermjakob,H., Kel,A.E., Kel,O.V., Ignatieva,E.V., Ananko,E.A., Podkolodnaya,O.A., Kolpakov,F.A., Podkolodny,N.L., and Kolchanov,N.A. (1998) Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. Nucleic Acids Res., 26, 362-367.
4. Kel,O.V., Romaschenko,A.G., Kel,A.E., Wingender,E., and Kolchanov,N.A. (1997) Composite regulatory elements: classification and description in the COMPEL database. Mol. Biol. (Mosk)., 31, 498-512.
5. Wingender,E., Kel,A.E., Kel,O.V., Karas,H., Heinemeyer,T., Dietze,P., Kn├╝ppel,R., Romaschenko,A.G., and Kolchanov,N.A. (1997) TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation. Nucleic Acids Res., 25, 265-268.
6. Kel,O.V., Romaschenko,A.G., Kel,A.E., Wingender,E., and Kolchanov,N.A. (1995) A compilation of composite regulatory elements affecting gene transcription in vertebrates. Nucleic Acids Res., 23, 4097-4103.
7. Matys,V., Fricke,E., Geffers,R., GÖßling,E., Haubrock,M., Hehl,R., Hornischer,K., Karas, D., Kel,A.E., Kel-Margoulis,O.V., Kloos,D.U., Land,S., Lewicki-Potapov,B., Michael,H., MÜnch,R., Reuter,I., Rotert,S., Saxel,H., Scheer,M., Thiele,S., and Wingender,E. (2003) TRANSFAC: transcriptional regulation, from patterns to profiles, Nucleic Acids Res., 31, 374-378.


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