NOVEL PRINCIPLES OF MOLECULAR GENETIC MAPPING OF THE INTERPHASE GENOME OF Drosophila melanogaster

Genome and chromosome maps have played a great role in the development of molecular genetics and biology. Gene activation, expression, and inactivation directly depend on the chromosomal (protein, nucleosomal) environment of the gene and formation of specific protein complexes on various gene structures. Polytene chromosomes are the only object in which interphase chromosomes can be analyzed, but the known Drosophila genome maps provide only an abstract view of gene distribution on a physical map, and there is no connection between these genes and the structures of interphase polytene chromosomes. A combination of bioinformatic methods was applied in this study; the data on interphase distribution of chromatin, H3K36me3 histone modifications, and the insulator protein Chriz, as well as the ChIP-seq, FAIRE-seq, and FISH methods, were used to investigate the genome-wide localization of key marker proteins. Having combined these mapping techniques for the small region 1AF of the X chromosome, we developed a novel method for analyzing the mutual arrangement of developmental and housekeeping genes, their promoters, and various types of proteins in the interphase genome and chromosome structures: compacted black bands, interbands, and gray bands, as well as sites of localization of exons and introns of housekeeping genes. Mapping was based on three consecutive stages: the 4 state Hidden Markov Model (hereinafter referred to as 4HMM) and data distribution for H3K36me3 and Chriz from the cells in which polytene chromosomes had been formed were used to localize interbands; FISH probes were then prepared from interband DNA, and blocks of developmental and housekeeping genes in interphase chromosome structures were mapped. The elaborated mapping methods can be further used to build similar maps for the entire interphase genome of Drosophila . Comparison of the map of bands and interbands in the region 1AF revealed full matching of the boundaries of black bands (developmental genes) and TADs. Within the regions where the housekeeping genes are located (the groups of interbands and gray bands), the TADs is formed on the basis of a gene cluster (the interband–gray band complex).