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Classic polythene chromosomes from dipteran insects are extensively used as a model for interphase chromosomes. The peculiar morphology of polythene chromosomes is formed by the alternating densely packed chromatin of bands and less compact interbands. In recent years numerous data have been obtained on the precise localization of different proteins on the molecular map in the interphase chromosomes. A special algorithm has been developed based on the interband specific protein composition. This algorithm allows us to detect the positions of bands and interbands in the whole Drosophila’s genome. The goal of our investigation is to analyse of P-elements distribution in localized bands and interbands. We have found that P-elements distribution is not random in Drosophila’s genome. Insertions of P-elements predominantly take place in regions of genome predicted by algorithm as interbands. The density of P-element insertions in compacted bands is notably lower.

As a result of treatment of bioinformatic data on the genome localization of structural proteins, histone modifications, DNase-hypersensitive regions, replication origins (taken from modENCODE) and their cytological localization to polytene chromosome structures, it is shown here that two types of interphase chromosomes -polytene chromosomes from salivary glands and from mitotically dividing cells cultures - demonstrate identical pictures of interband/band, i. e. the same localization and length on physical map and the same sets of proteins. In the interbands of both chromosome types we find the proteins that control initiation of transcription (RNA-polymerase II, transcription factors), replication (ORC2) as well as proteins modifying nucleosome structure (WDS, NURF) and proteins of insulators (BEAF). The nucleosome density and H1 histone concentration in the interbands are depleted; localization of DNase-hypersensitive regions corresponds strictly to the interbands. So, we conclude that both polytene and cell line interphase chromosomes are arranged according to general principle and polytene chromosomes represent precise model of interphase chromosomes. The interbands play a critical role in the initiation of transcription and replication. The interbands of interphase chromosomes are the sites of 5' parts of genes, while the 3' gene ends are located in the adjacent bands. The constancy of interbands decondensation results in the conclusion that the "interbands" genes are constantly active, i. e. they contain "house-keeping" genes. The large late replicating bands contain genes that do not have direct contact to the adjoining interbands are usually polygenic and contain tissue-specific genes.