Functional architecture of chromosomal DNA domains

More than 20 years ago, it was found that chromosomal DNA in eukaryotic cell nuclei was organized into large loops by periodic attachment to the high salt-insoluble proteinous nuclear (chromosomal) matrix. The specificity of genomic DNA partitioning into loops has been studied intensively trying to find out whether loops may constitute quasiindependent structural-functional units of the genome. These studies have resulted in conflicting findings and, consequently, in conflicting conclusions. Recently, we have developed a conceptually new approach for analysis of specificity of the DNA loop organization by topoisomerase II-mediated excision of individual loops and their oligomers. Using this approach we have obtained new data supporting the supposition that loops may constitute the basic units of genome organization and evolution. In the present article we critically analyze all existing data on specificity and functional significance of chromosomal DNA organization into loops. The goals of this analysis are: 1. To evaluate the available experimental data and try to understand the reasons of the conflicting results obtained by different experimental approaches. 2. Try to answer the long-standing question about a possible correlation between the functional organization of the genome and the mode of its packaging within the nuclei.