Spatial distribution of GC- and AT-rich DNA sequences within human chromosome territories

Previous topological analyses of DNA sequence organization in the interphas e chromosome mainly focused on the spatial distribution of individual gene copies within chromosome territories. In order to achieve a more comprehens ive view into the subchromosomal arrangement of DNA, we isolated the GC-ric hest/gene-richest fraction (H3 isochores) as well as AT-richest/gene-poores t fraction of human genomic DNA (L1+L2 isochores) and visualized the respec tive DNA within individual chromosome territories by means of dual-color FI SH. Application of confocal laser scanning microscopy and dedicated 3D imag e analysis software, which differentiated territory subvolumes by peeling s hells one voxel in width, revealed a significant difference in the intrater ritorial distribution of these two DNA sequence classes. While the H3 isoch ores were found localized in all subvolumes of the territories at similar f requency, simultaneously detected L1+L2 isochores were observed more to the interior of the same chromosome territories. Thus the GC-rich sequences di splay a much higher variability in their intraterritorial localization than AT-rich DNA fragments. (C) 2000 Academic Press.