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The study spatial chromosome structure and chromosome folding in the interphase cell nucleus is an important  challenge of world science. Detection of eukaryotic genome regions that physically interact with each other could be  done by modern sequencing technologies. A basic method of chromosome folding by total sequencing of contacting  DNA fragments is HI-C. Long-range chromosomal interactions play an important role in gene transcription  and regulation. The study of chromosome interactions, 3D (three-dimensional) genome structure and its effect  on gene transcription allows revealing fundamental biological processes from a viewpoint of structural regulation  and are important for cancer research. The technique of chromatin immunoprecipitation and subsequent sequencing  (ChIP-seq) make possible to determine binding sites of transcription factors that regulate expression of eukaryotic  genes; genome transcription factors binding maps have been. The ChIA-PET technology allows exploring  not only target protein binding sites, but also pairs of such sites on proximally located and interacting with  each other chromosomes co-located in three-dimensional space of the cell nucleus. Here we discuss the principles  of the construction of genomic maps and matrices of chromosome contacts according to ChIA-PET and Hi-C data that  capture the chromosome conformation and overview existing software for 3D genome analysis including in house  programs of gene location analysis in topological domains.

Computer methods of analysis of chromosome contacts in the cell nucleus based on sequencing technology data