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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.

Genetic activity of interphase chromosomes is associated with their structural organization, but the mechanism of these relations is still unclear. Classic polythene chromosomes of dipteran insects are a convenient model for such investigations. Despite intensive study of polythene chromosomes of Drosophila melanogaster is carried out, an exact conformity of bands and interbands to the molecular map of the genome remains unknown in most cases. For addressing this issue, the genetic map and molecular characteristics of chromatin have been compared with the banding pattern of the fourth chromosome, which is the smallest chromosome in the D. melanogaster genome and is different in many ways from other chromosomes. This is a unique chromatin domain of D. melanogaster, which is characterized by specific proteins, including HP1, POF and EGG. Matching of cytological and physical maps of the fourth chromosome has been carried out by FISH. Genomic coordinates of bands and interbands have been determined. This result makes it possible to investigate the regulation of gene activity of the fourth chromosome in the context of molecular characteristics of cytological structures in which these genes are located.

Drosophila melanogaster polytene chromosomes display specific banding pattern; the underlying genetic organization of this pattern has remained elusive for many years. In the present paper, we analyze 32 cytology-mapped polytene chromosome interbands. We estimated molecular locations of these interbands, described their molecular and genetic organization and demonstrate that polytene chromosome interbands contain the 5' ends of housekeeping genes. As a rule, interbands display preferential "head-to-head" orientation of genes. They are enriched for "broad" class promoters characteristic of housekeeping genes and associate with open chromatin proteins and Origin Recognition Complex (ORC) components. In two regions, 10A and 100B, coding sequences of genes whose 5'-ends reside in interbands map to constantly loosely compacted, early-replicating, so-called "grey" bands. Comparison of expression patterns of genes mapping to late-replicating dense bands vs genes whose promoter regions map to interbands shows that the former are generally tissue-specific, whereas the latter are represented by ubiquitously active genes. Analysis of RNA-seq data (modENCODE-FlyBase) indicates that transcripts from interband-mapping genes are present in most tissues and cell lines studied, across most developmental stages and upon various treatment conditions. We developed a special algorithm to computationally process protein localization data generated by the modENCODE project and show that Drosophila genome has about 5700 sites that demonstrate all the features shared by the interbands cytologically mapped to date.