Recent developments of 4D (space-time) live cell microscopy (1), 3D light optical nanoscopy with resolution beyond the classical Abbe limit (2 - 6) and advanced electron microscopic approaches (7 - 8) complement each other in studies of the functional nuclear architecture (for review see 9). The results of these studies support the chromosome territory-interchromatin compartment model of nuclear architecture (10 - 13).

Chromosome territories (CTs) occupy distinct regions of the nuclear space. They are built up from a network of interconnected chromatin domains with a DNA-content in the order of 1 Mb, termed ~1Mb CDs. The structure of ~1Mb CDs has not yet been resolved, but we argue that each ~1Mb CD is built up from a series of more or less compacted chromatin loop domains with a DNA content in the order of 100 kb, termed ~100 kb CDs. Moreover, several ~1Mb CDs can cluster together and form larger CDs. During S-phase replicating ~1Mb CDs act as replication foci. Direct contacts between neighboring ~1Mb CDs provide ample opportunities for interactions in cis (within a given CT) or trans (between neighboring CTs), including the formation of intra- and interchromosomal rearrangements. Beyond the nucleosome and the 10 nm thick, ‘beads on a string’ chromatin fiber, we lack indisputable, quantitative evidence for possible hierarchies of higher order chromatin fibers and loops. In particular, we do not know the extent of quantitative variation possible with regard to the size distributions and extent of intermingling of fibers and loops at different hierarchical levels in different cell types of different species exposed to different internal or external stimuli. To which extent interactions between giant chromatin loops expanding from widely separated CTs are involved in the relocalization of genes to specialized subnuclear compartements (“gene kissing”), is still controversially discussed. Based on our current knowledge, we expect that such events are mostly driven by locally constrained Brownian movements.



Figure 1: This 2D cartoon shows a simplified scheme of the more complex 3D nuclear architecture. CDs are not drawn to scale (adapted from Fig. 4 in T. Cremer and M. Cremer, 2010).

The perichromatin region (PR) represents a 100 - 200 nm thick layer of decondensed chromatin, located at the periphery of CDs. It constitutes the nuclear compartment for transcription, splicing, DNA-replication and possibly also DNA-repair (6 - 8, 9). The PR is in direct contact with the interchromatin-compartment (IC), which forms an interconnected 3D system of IC-channels (width <400 nm) and IC-lacunas (width >400 nm). It starts/ends with small channels at the nuclear pores and expands both between CTs and throughout the interior of CTs. Accordingly the 3D organization of a CT can be compared with a sponge built up from a 3D chromatin network permeated by the IC (Fig. 1)(6, 13). It should be noted that constrained Brownian movements of CDs in the nucleus of living cells (1) result in continuous changes of the width of IC channels providing dynamic opportunities for normal or pathological interactions. The interior of IC lacunas is free of chromatin and harbors nuclear bodies and splicing speckles (6, 7). This structural organization allows direct functional interactions between the IC and the PR, such as the delivery of splicing components from splicing speckles to sites of co-transcriptional splicing (Fig. 1). Although individual proteins may be able to diffuse through the whole nuclear space, including heterochromatic domains, it still seems to be a valid possibility that the IC and the PR represent specific nuclear compartments for the intranuclear traffic of protein complexes involved in nuclear functions and the export ribonucleoprotein complexes.

References

1. H. Strickfaden Nucleus 1, 284-297 (2010)
2. L. Schermelleh et al. Science 320, 1332-1336 (2008)
3. M. Gunkel et al. Biotechnol J 4, 927-938 (2009)
4. D. Baddeley et al. Nucleic Acids Res 38, e8 1-11 (2010)
5. C. Cremer et al. In: Nanoscopy and Multidimensional Optical Fluorescence Microscopy (A. Diaspro, Edit.) Taylor & Francis, pp. 3/1 – 3/35 (2010).
6. Y. Markaki et al. Cold Spring Harb Sym Quant Biol 75, in press (2011).
7. J. Rouquette et al. Chromosome Res 17, 801-810 (2009).
8. J. Niedojadlo et al. Exp Cell Res 317 433-444 (2011).
9. J. Rouquette et al. Int Rev Cell Mol Biol 282, 1-90 (2010).
10. T. Cremer, et al. Crit Rev Eukar Gene 10, 179-212 (2000).
11. T. Cremer, T. and C. Cremer. Nat Rev Genet 2, 292-301 (2001).
12. C. Lanctôt et al. Nat Rev Genet 8, 104-115 (2007).
13. T. Cremer and M. Cremer Cold Spring Harb Perspect Biol 2 a003889 (2010).