The nucleus appears to be organized according to the many functions it performs [1
]. The nucleolus, for example, is a subcompartment that exists as a result of its activities: rDNA transcription and ribosomal biogenesis [1
]. Gene loci reflect this functional organization in that their subnuclear localization often correlates with their expression status. Among many examples, it has been demonstrated that: (1) silent loci positioned at the nuclear periphery relocalize to the nuclear center when activated during cellular differentiation (e.g., [3
]); (2) subsets of expressed genes from a single chromosome territory (CT) colocalize in transcription factories [5
]; and (3) the regulation of cell-type–specific genes correlates with their association in the nucleus, despite being found on different chromosomes [6
]. In addition, gene loci are often localized relative to their respective CT, with active gene domains looped away from the territory and inactive domains at its surface (e.g., [7
]). These observations and others have rekindled interest in a long-standing question in the study of nuclear organization: do chromosomes have defined positions within the nucleus?
Structural arrangements of chromosomes, such as the Rabl configuration and the prometaphase rosette, have been known for some time, and there are recent examples of the nonrandom organization of chromosomes [9
]. Although it has become clear that nuclear organization is inherently probabilistic, the tendencies for certain chromosomes to be preferentially localized within the nucleus have been demonstrated. For example, analysis of the radial positioning of individual CTs within human nuclei revealed that gene-dense chromosomes have a propensity to be centrally localized, whereas gene-poor chromosomes are more peripheral [10
]. This phenomenon has also been observed in the nuclei from other primates [13
]. An examination of the organization of all chromosomes within individual human nuclei, however, did not reveal a consistent role for gene density in CT localization [14
]. Rather, this analysis determined that a chromosome's size (as a function of its overall length) is also related to its radial positioning, with small chromosomes being found more centrally positioned. Similar results were observed in an analysis of mouse nuclei [15
]. The varying impact of chromosome density and size may be due to cell-type differences or to the method of analysis (e.g., focusing on a chromosome's center of gravity as opposed to its total area or volume). Nevertheless, a common basis for nonrandom chromosome organization beyond basic chromosome characteristics such as gene density or overall length has yet to be elucidated.
Analysis of genomes from multiple species has revealed that genes have a particular linear arrangement along chromosomes: the co-regulated genes of transcriptomes have a marked tendency to be found grouped (or clustered) according to their shared expression status [2
]. Therefore, gene loci not only localize to positions within the nucleus relevant to their expression, but they are also inherently organized nonrandomly along chromosomes. It is unclear what function this clustering of genes plays, although the prevailing model suggests that clusters create expression “hubs” or “neighborhoods” in which the linearly proximal genes alter the dynamics of regulatory protein (transcription factor) binding by increasing the relative abundance of binding sites [19
]. Given that hundreds of genes are regulated during cellular differentiation, the localization of individual gene clusters may be reflected in the organization of chromosomes enriched in these co-regulated genes [20
]. Specifically, chromosomes may be organized in relation to their total, cell-specific expression profile. This organization may involve nuclear localization of chromosome territories, interchromosomal interactions, or both.
We have used an in vitro model of murine hematopoiesis to test the hypothesis that cellular differentiation is associated with a relationship between the linear arrangement of co-regulated genes and chromosomal organization. FDCPmix cells are nontransformed, multipotential hematopoietic progenitors that can be maintained and differentiated into a number of blood cell lineages—including highly pure populations (~90%) of erythrocytes and neutrophils—with the appropriate cytokines [21
]. To explore the possibility of a link between gene expression and genomic organization, we determined the linear chromosomal arrangement of co-regulated genes and the organization of chromosomes for the three cell types. Our results demonstrate a relationship between the chromosomal distribution of co-regulated genes and the propensity for homologous chromosomes and co-regulated gene domains to be proximal. We suggest that the spatial proximity of genes along chromosomes and the association of homologous chromosomes help ensure the coordinate regulation of genes during cellular differentiation.