Spatio-temporal dynamics of genomic organization and function in the mammalian cell nucleus

A new view of the mammalian cell nucleus is emerging based on genomic function and interrelationships with nuclear architecture. We previously proposed a model for the organization of gene replication and transcription in the cell nucleus which involves zoning and higher order networking of the individual chromatin domains that constitute these functional sites. This higher order networking of replicational and transcriptional activity may represent the structural underpinning for the functional programming and coordination of replication and transcription processes in the cell. In this article we summarize our progress using computer imaging to study the higher order arrangement of chromatin domains in relation to function and their dynamics in living cells. Newly developed algorithms that directly evaluate network structure demonstrate elaborate but spatially separate networks for early S labeled replication and transcription sites following dual labeling experiments. We further demonstrate that chromatin domains in living cells derived from DNA replicated in early S-phase show a striking degree of translational motion and configurational (shape) changes. In particular, transitions of chromatin domains were observed between discrete to more diffusely labeled sites. Since transcriptional activity is preferentially associated with the diffusely labeled regions of chromatin, these configurational changes in chromatin domains of living cells may be indicative of dynamic transitions between transcriptionally active and inactive states of the chromatin. In agreement with this hypothesis, chromatin domains containing DNA replicated in mid or late S-phase which are much less active transcriptionally, show much lower levels of both movement and shape changes. Moreover, observations of living HeLa cells stably transfected with GFP-PCNA indicate that the dynamics of chromatin domains is maintained at a similar level during active DNA replication in early S-phase.