Nuclear organization of mammalian genomes: polar chromosome territories build up functionally distinct higher order compartments

We investigated the nuclear higher order compartmentalization of chromatin according to its replication timing (Ferreira et al., 1997) and the relatio ns of this compartmentalization to chromosome structure and the spatial org anization of transcription. Our aim was to provide a comprehensive and inte grated view on the relations between chromosome structure and functional nu clear architecture. Using different mammalian cell types, we show that dist inct higher order compartments whose DNA displays a specific replication ti ming are stably maintained during all interphase stages. The organizational principle is clonally inherited. We directly demonstrate the presence of p olar chromosome territories that align to build up higher order compartment s, as previously suggested (Ferreira et al., 1997). Polar chromosome territ ories display a specific orientation of early and late replicating subregio ns that correspond to R- or G/C-bands of mitotic chromosomes. Higher order compartments containing G/C-bands replicating during the second half of the S phase display no transcriptional activity detectable by BrUTP pulse labe ling and show no evidence of transcriptional competence. Transcriptionally competent and active chromatin is confined to a coherent compartment within the nuclear interior that comprises early replicating R-band sequences. As a whole, the data provide an integrated view on chromosome structure, nucl ear higher order compartmentalization, and their relation to the spatial or ganization of functional nuclear processes.