The binding sites of the proteins regulating transcription in the early development of Drosophila melanogaster: A comparative analysis of ChIP-chip data and theoretically predicted clusters

For six proteins involved in transcriptional regulation of the early embryonic development of Drosophila melanogaster, DNA regions with significant binding as determined by chromatin immunoprecipitation with subsequent hybridization on a biochip (the ChIP-chip method) were considered. At the same time, binding site clusters of these proteins were predicted computationally. The theoretical and experimental data were compared for all pairwise combinations of factors studied. For chromosome 2R, it was shown that the intensity of the ChIP-chip signal differed significantly between the regions within and outside the predicted binding site clusters. In spite of the difficulties caused by the ChIP-chip signal noise, comparison of the experimental data in various pairwise combinations indicated that certain factors tend to bind in the same DNA regions, which supports the evidence of their functional association. Therefore, comparison of ChIP-chip data with the results of sequence analysis can reveal functionally interconnected regulatory subsystems even in systems studied less comprehensively than the system of regulation of the early embryonic development of D. melanogaster.