Background: The eukaryotic genome evolves under the dual constraint of maintaining co-ordinated gene transcription and performing effective DNA replication and cell division, the coupling of which brings about inevitable tension in DNA topology. This is resolved and in some cases even harnessed by the genome through the function of DNA topoisomerases, as has been shown in the concurrent transcriptional activation and suppression of genes upon transient deactivation of topoisomerase II and distinct areas of the genome are expected to be differentially affected by DNA topological constraints. The scope of this work is to identify positional and structural preferences in the distribution of genes, relative to their response to topo-II deactivation. Results: By analyzing a genome wide run-on experiment upon thermal inactivation of topo II in S. cerevisiae we were able to define 117 gene clusters of concerted response (either positive or negative) to topological stress. A comprehensive analysis of these "topologically co-regulated" gene clusters revealed pronounced preferences regarding their functional, regulatory and structural attributes. Our findings point towards a particular genome compartmentalization, according to which genes that negatively respond to topological stress, are positioned in gene-dense pericentromeric regions, are more conserved and associated to essential functions, while up-regulated gene clusters are preferentially located in the gene-sparse nuclear periphery, associated with secondary functions and under complex regulatory control. Conclusions: This multi-faceted division of labour is much resembling a "genome urbanization" process with a core of essential genes occupying a compact genomic "old town", whereas more recently acquired, condition-specific genes are located in a more spacious "suburban" genomic periphery.