Artsite Database: Comparison of In Vitro Selected and Natural Binding Sites of Eukaryotic Transcription Factors

Abstract

The ArtSite database was developed; the database compiles the information on the structures of eukaryotic transcription factor binding sites and/or their DNA-binding domains obtained from in vitro selected sequences. Current release of the database comprises 420 matrices describing specific features of binding sites or their DNA-binding domains for over 200 transcription factors. The matrices were constructed basing on alignments of representative samples of transcription factor binding sites, totally containing over 10 thousand sequences.

The information compiled in ArtSite was used to compare the structures of natural and in vitro selected binding sites for USF1, SP1, YY1, RAR/RXR, and E2F/DP1 transcription factors. The structures of the natural and in vitro selected binding sites for each transcription factor analyzed were found similar, suggesting that at least for the factors in question the structures of binding sites correlated with the affinities of the corresponding factors. Insignificant differences in detected frequencies of certain nucleotides reflect the general trend, namely, a higher occurrence of moderate affinity sites in the natural population of sequences compared with the sequences obtained in vitro.