[Preferred distances between DNA binding sites for factors regulating transcription initiation].

Transcriptional regulation of gene expression in higher eukaryotes is driven by sophisticated protein complexes of transcription factors. On the DNA level, there are composite elements containing sites of different DNA-binding proteins. We use the hypoxia-response system to identify preferred localization distances for the 'hypoxia-induced factor-1 binding site-co-factor binding site" pairs in promoter DNA regions of the human genome. Such characteristic colocalization distances agree with the supposed scale of regulatory regions, while being significantly longer than the typical binding site length. We speculate that this phenomenon can provide a key to decipher the structure of DNA regulatory regions of higher eukaryotes.

[Integration of data obtained by different experimental methods to determine the motifs in DNA sequences recognized by transcription-regulating factors].

For 39 proteins regulating the transcription of Drosophila melanogaster, refined motifs typical for nucleotide sequences specifically interacting with these proteins have been constructed using the new logarithm ChiPMunk. The entire spectrum of available experimental data, including the data of DNAse footprinting, SELEX, ChIP-chip, and B1H-system, has been used. Motifs constructed by integrating the data obtained by independent experimental methods show the highest sensitivity. The collection of motifs can be used to refine the immediate binding sites of transcription factors in DNA nucleotide sequences. The collection of motifs and the results of the estimation of motif quality are available at: http://line.imb.ac.ru/iDMMPMM. The realization of the algorithm ChIPmunk is accessible at http://line.imb.ac.ru/Chipmunk.