To test the hypothesis that the nonrandom organization of the contents of interphase nuclei represents a compartmentalization of function, we examined the relative, spatial relationship of small nuclear ribonucleoproteins (snRNPs) and of DNase I hypersensitive chromatin (DHC) in rat pheochromocytoma cells. In controls, DHC and snRNPs colocalized as pan-nuclear speckles. During nerve growth factor-induced differentiation, both snRNPs and DHC migrated to the nuclear periphery with the migration of DHC preceding that of snRNPs, resulting in their transient separation. The formation of DHC shells temporally coincided with an up-regulation of neurofilament light chain mRNA., This indicates that the expression of this sequence may be associated with its spatial transposition to the nuclear periphery.The molecular factors controlling RNA synthesis, processing, and transport occupy distinct, subnuclear regions in interphase nuclei. This has led to the concept that nuclei are topologically organized and that one level of control of gene expression is exerted by spatially coupling transcription and RNA processing (1-5). The scope of investigation of processes that control gene expression has thus expanded beyond molecular mechanisms to include transcription-associated changes in the supramolecular topology of nuclei. This concept of functional, nuclear compartmentalization is supported by the finding that factors involved in transcript processing, including small nuclear ribonucleoproteins (snRNPs) and the non-snRNP factor SC35, form discrete foci in nuclei, known as speckles (6-9). Also, specific chromosomes and specific domains thereof, including centromeric DNA, transcribed sequences as well as aggregates of RNA processing factors, are arranged in distinct, spatial relationships (1, 10-13). Although transcription occurs throughout nuclei in some cell types (14,15), other evidence suggests that compartmentalization also applies to sites of transcription, represented by distinct, pan-nuclear foci of DNase I hypersensitive chromatin (DHC), a distribution that can be modulated by changes in cell function (16)(17)(18)(19)(20)(21)(22). Although DHC structurally represents all nucleosome-free DNA, regardless of transcriptional state, it does include transcriptionally active sequences (23,24).DHC (16,(18)(19)(20)(21)(22) and such nonexpressed sequences as centromeric DNA (25-28) and snRNP foci (8) change position under conditions that change gene expression. This indicates that changes in nuclear compartmentalization and gene expression may be functionally linked. We now report that differentiation of rat pheochromocytoma (PC12) cells is associated with a temporally out-of-phase transposition of DHC and snRNPs to the nuclear periphery, and that associated changes in gene expression. temporally coincide with the transposition of DHC, but not with that of snRNPs. MATERIALS AND METHODSCell Culture. PC12 cells were seeded on glass coverslips coated with rat tail collagen (type VII; Sigma), and maintained in a medium consis...

DNAse sensitive chromatin, putative transcriptionally competent sequences, exists either as pan-nuclear speckles in cells with nuclei which exhibit a flat geometry, or as a shell apposed to the nuclear envelope in cells with spheroidal nuclei. To test the hypothesis that DNAse sensitive chromatin is similarly associated with the nuclear periphery in cell types with a very flat geometry such as 3T3 fibroblasts, cells were subjected to hypotonic expansion to change their nuclei from a flat ellipsoid to a spheriod. This was based on the assumption that such a spatial association is not resolvable due to the interdigitation at the nuclear midplane of DNAse sensitive chromatin associated with the upper and lower nuclear surfaces. In situ nick translation was used to visualize the distribution of DNAse sensitive chromatin as a function of nuclear geometry. Both unexpanded and expanded cells exhibit DNAse sensitive chromatin as a dome at the apical side of the nucleus, i.e., that aspect of the cell facing the culture medium. The results argue for a polarized association of DNAse sensitive chromatin with the nuclear envelope and indicate that the nuclear periphery may function as a compartment for the spatial coupling of transcription and nucleo-cytoplasmic transport.