A comparative analysis of the binding sites of proteins regulating the transcription in the early development of Drosophila melanogaster, determined by the ChIP-chip method and the theoretically predicted clusters of the binding sites of these proteins

DNA segments were analyzed for six proteins regulating the transcription in the early embryonic development of Drosophila melanogaster in which a significant binding of these proteins was observed by the method of immunoprecipitation of chromatin followed by the precipitation on the template (Chip-chip). The regions of high density of the theoretically predicted binding sites of these proteins in these fragments were considered. A comparison of the experimental and theoretical data for various pairwise combinations of the above-mentioned factors was made. It was shown that the intensity of data obtained by the ChiP-chip method significantly differs outside and inside identified clusters. A comparison of experimental data in various pairwise combinations of the factors showed that, despite the problems associated with a great noise in the ChiP-chip signal, a strong tendency of particular groups of factors to bind in the same DNA regions was revealed, which is consistent with the data about their functional coupling. Thus, a comparison of the data obtained by the ChiP-chip method makes it possible to distinguish functionally related regulatory subsystems even in the case of systems that are much less investigated than the system of the early embryonic development of Drosophila melanogaster.