The major functions of the cell nucleus, including transcription, pre-mRNA splicing and ribosome assembly, have been studied extensively by biochemical, genetic and molecular methods. An overwhelming amount of information about their molecular mechanisms is available. In stark contrast, very little is known about how these processes are integrated into the structural framework of the cell nucleus and how they are spatially and temporally co-ordinated within the three-dimensional confines of the nucleus. It is also largely unknown how nuclear architecture affects gene expression. In order to understand how genomes are organized, and how they function, the basic principles that govern nuclear architecture and function must be uncovered. Recent work combining molecular, biochemical and cell biological methods is beginning to shed light on how the nucleus functions and how genes are expressed in vivo. It has become clear that the nucleus contains distinct compartments and that many nuclear components are highly dynamic. Here we describe the major structural compartments of the cell nucleus and discuss their established and proposed functions. We summarize recent observations regarding the dynamic properties of chromatin, mRNA and nuclear proteins, and we consider the implications these findings have for the organization of nuclear processes and gene expression. Finally, we speculate that self-organization might play a substantial role in establishing and maintaining nuclear organization.

Abbreviations used: GFP, green fluorescent protein; CB, Cajal body; RNA pol II; RNA polymerase II; SFC, splicing-factor compartment; rDNA, ribosomal genes; DFC, dense fibrillar components; snRNP, small nuclear ribonucleoprotein particle; snoRNP, small nucleolar ribonucleoprotein particle; snRNA, small nuclear RNA; snoRNA, small nucleolar RNA; PNB, pre-nucleolar body; SRP, signal-recognition particle; MDM2, murine double minute clone 2 oncoprotein; PML, promyelocytic leukaemia oncoprotein; APL, acute promyelocytic leukaemia; PNC, perinucleolar compartment; FRAP, fluorescence recovery after photobleaching; GR, glucocorticoid receptor.

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