Novel Principles of Molecular Genetic Mapping of the Interphase Genome of Drosophila melanogaster

A novel method for mapping the interphase genome architecture in Drosophila polytene chromosomes is proposed. The method is based on physical mapping of the boundaries between interbands, gray bands, and black bands. Mapping relies on three criteria: the 4HMM bioinformatic model that considers the associations between each of the four chromatin states and polytene chromosome structures and the findings of ChIP-seq analysis in salivary glands for two critical markers: the CHRIZ/CHRO protein localized in housekeeping gene promoters and H3K36me3 histone modification, a marker of transcriptional elongation. For mapping the 1AF region of the X chromosome, FISH probes were selected from AQUAMARINE chromatin (interbands) at the boundary with black bands, which provided precise coordinates of the edges of black bands (localization of the developmental genes). The localization of promoters and housekeeping gene bodies was then identified by ChIP-seq analysis for CHIRIZ and H3K36me3 in salivary glands (the interbands and gray bands, respectively). These maps will allow one to better understand the architecture of an actively functioning genome.