COMPOSITE REGULATORY ELEMENTS - CLASSIFICATION AND DESCRIPTION IN THECOMPEL DATABASE

The COMPEL database was developed to compile information on composite regulatory elements revealed in the regulatory regions of eukaryotic g enes transcribed by RNA polymerase II. The composite elements contain two adjacent binding sites for various transcription factors, and are minimal functional units that regulate transcription in a highly speci fic way through specific DNA-protein and protein-protein interactions. Each entry in the database corresponds to one composite element and c ontains data on its sequence and location, as well as description of f eatures of regulation by this element. The elements can be classified into synergistic and antagonistic according to the type of interaction between the transcription factors involved. Within the synergistic ty pe of composite elements, two transcription factors bind simultaneousl y to their target sites and activate transcription cooperatively. With in the antagonistic type, the factor inhibiting transcription either d isplaces the activating factor and competes with it for the binding si te or, simultaneously binding to DNA, inhibits the activating factor's activity in a different way, At present, COMPEL describes 146 composi te elements of the synergistic (118) and antagonistic (28) type in 79 different genes of vertebrates and their viruses. The database is link ed by cross-references with other transcription regulation databases, TRRD and TRANSFAC. In the present work we describe the COMPEL format, discuss criteria used for revealing composite elements, propose classi fication of composite elements based on the character of their regulat ory action on transcription, and consider structure and possible mecha nisms of functioning of some groups of composite elements, COMPEL is e lectronically accessible (ftp://transfac.gbf-braunschweig.de/pub/compe l/ and http://www.bionet.nsc.ru/COMPEL).