The dynamic compartmental organization of the transcriptional machinery in mammalian nuclei places particular constraints on the spatial organization of the genome. The clustering of active RNA polymerase I transcription units from several chromosomes at nucleoli is probably the best-characterized and universally accepted example. RNA polymerase II localization in mammalian nuclei occurs in distinct concentrated foci that are several-fold fewer in number compared to the number of active genes and transcription units. Individual transcribed genes cluster at these shared transcription factories in a nonrandom manner, preferentially associating with heterologous, coregulated genes. We suggest that the three-dimensional (3D) conformation and relative arrangement of chromosomes in the nucleus has a major role in delivering tissue-specific gene-expression programs.