Spatial relationship between transcription sites and chromosome territories

We have investigated the spatial relationship between transcription sites a nd chromosome territories in the interphase nucleus of human female fibrobl asts. Immunolabeling of nascent RNA was combined with visualization of chro mosome territories by fluorescent in situ hybridization (FISH). Transcripti on sites were found scattered throughout the territory of one of the two X chromosomes, most likely the active X chromosome, and that of both territor ies of chromosome 19. The other X chromosome territory, probably the inacti ve X chromosome, was devoid of transcription sites. A distinct substructure was observed in interphase chromosome territories. Intensely labeled subch romosomal domains are surrounded by less strongly labeled areas. The intens ely labeled domains had a diameter in the range of 300-450 nm and were some times interconnected, forming thread-like structures. Similar large scale c hromatin structures were observed in HeLa cells expressing green fluorescen t protein (GFP)-tagged histone H2B, Strikingly, nascent RNA was almost excl usively found in the interchromatin areas in chromosome territories and in between strongly GFP-labeled chromatin domains. These observations support a model in which transcriptionally active chromatin in chromosome territori es is markedly compartmentalized. Active loci are located predominantly at or near the surface of compact chromatin domains, depositing newly synthesi zed RNA directly into the interchromatin space.