Plant & Animal Genome V Conference
Town & Country Hotel, San Diego, CA, January 12-16, 1997.
PAG-V: W58 - A CLASSIFICATION SCHEME FOR EUKARYOTIC TRANSCRIPTION FACTORS
W58
A CLASSIFICATION SCHEME FOR EUKARYOTIC TRANSCRIPTION FACTORS
WINGENDER, EDGAR
Gesellschaft fuer Biotechnologische Forschung mbH, Mascheroder Weg 1, D-38124 Braunschweig
As a tool for the functional interpretation of genomic sequences, we have established the TRANSFAC database on cis-acting elements and trans-acting factors. We are presently including a comprehensive classification of transcription factors which could give us a clue to systematic functional assignment of the regulatory signals within genomes. For this purpose, a classification scheme has been developed which focusses on DNA-binding transcription factors and their derivatives. It comprises six levels classifying these proteins according to (a) the general topology of the DNA-binding domain ("superclass" level; e. g. zinc-coordinating domains), (b) its structural principle ("class"; e. g. zinc finger motif of nuclear receptors), (c) functional criteria such as the mechanism of forming a DNA-protein complex ("family"; e. g., T3R/RAR vs. steroid hormone receptors), (d) the sequence similarity of the DNA-binding domains ("subfamily", such as RAR), (e) the transcription factor gene ("genus", such as RAR-beta), and (f) initiation/ splicing/ processing variants (factor "species", such as RAR-beta1). Presently, four large superclasses have been defined which comprise most, but not yet all transcription factors known so far. They are divided into 25 clearly defined classes which correspond to the classes used by and explained in the CLASS table of the TRANSFAC database.