Role of Chromosome Territories in the Functional Compartmentalization of the Cell Nucleus

Cremer, Thomas; Kurz, A.; Zirbel, R. M.; Dietzel, Steffen; Rinke, Bernd; Schröck, Evelin; Speicher, Michael R.; Mathieu, U. R.; Jauch, Anna; Emmerich, Patricia; Scherthan, Harry; Ried, Thomas; Cremer, Christoph; Lichter, Peter

doi:10.1101/sqb.1993.058.01.085

Cited by 455 publications

(319 citation statements)

References 85 publications

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“…Functional domains in nuclei are dependent on the three-dimensional (3-D) arrangement of the genes and proteins within the nuclear space (Cremer et al, 1993;Lawrence et al, 1993). It is clear that this arrangement is crucial to dictate gene activities in the nucleus, and it can be postulated that the 3-D arrangement of genes and associated transcription factors is a level of regulation of the transcription in the integrated structure of the nucleus.…”

Section: Introductionmentioning

confidence: 99%

Involvement of in situ conformation of ribosomal genes and selective distribution of upstream binding factor in rRNA transcription.

Junera

Masson

Géraud

et al. 1997

MBoC

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The distribution of the ribosomal genes (rDNA) and the upstream binding factor (UBF), correlatively with their RNA transcripts, was investigated in G1, S-phase, and G2. rDNA was distributed in nucleoli, with alternate sites of clustered and dispersed genes. UBF was found associated with some but not all clustered genes and proportionally more with dispersed genes. It was distributed in several foci that were more numerous and heterogeneous in size during G2 than G1. We suggest that UBF associated with rDNA during S-phase because its nucleolar amount increased during that time and remained stable in G2. 5,6-Dichloro-1-13-D-ribofuranosylbenzimidazole treatment indicated a similar amount of UBF per transcription unit, and consequently heterogeneous size of the UBF foci can represent a variable number of transcription units per foci. Direct visualization of the transcripts demonstrated that only part of UBF is associated with active transcription and that rDNA distribution varied with transcription. We propose that in the same rDNA locus three types of configuration coexist that are correlated with gene activity: 1) clustered genes without UBF; 2) clustered genes with UBF, of which some are associated with transcription; and 3) dispersed genes with UBF and transcription. These results support the hypothesis that rDNA transcription involved several steps of regulation acting successively and locally in the same locus to promote the repressed clustered genes to become actively transcribed dispersed genes.

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Section: Introductionmentioning

confidence: 99%

Involvement of in situ conformation of ribosomal genes and selective distribution of upstream binding factor in rRNA transcription.

Junera

Masson

Géraud

et al. 1997

MBoC

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“…During interphase, different chromosomes occupy different nuclear regions or Fterritories_ (Cremer et al 1993, 2000, Cremer & Cremer 2001, Bolzer et al 2005. Interphase chromosomes are highly dynamic, with active chromatin in an open conformation and undergoing continual exchange of protein components , Phair & Misteli 2000.…”

Section: Introductionmentioning

confidence: 99%

Micromechanical studies of mitotic chromosomes

2008

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Mitotic chromosomes respond elastically to forces in the nanonewton range, a property important to transduction of stresses used as mechanical regulatory signals during cell division. In addition to being important biologically, chromosome elasticity can be used as a tool for investigating the folding of chromatin. This paper reviews experiments studying stretching and bending stiffness of mitotic chromosomes, plus experiments where changes in chromosome elasticity resulting from chemical and enzyme treatments were used to analyse connectivity of chromatin inside chromosomes. Experiments with nucleases indicate that non-DNA elements constraining mitotic chromatin must be isolated from one another, leading to the conclusion that mitotic chromosomes have a chromatin Fnetwork_ or Fgel_ organization, with stretches of chromatin strung between Fcrosslinking_ points. The as-yet unresolved questions of the identities of the putative chromatin crosslinkers and their organization inside mitotic chromosomes are discussed.

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“…The diffusion of molecules within the nucleus is obstructed by the steric constraints imposed by structural components, such as chromatin (6,7). Proposed models for 3D arrangement of chromatin vary from defined regions of chromatin compartmentalisation (8) to intermingled chromatin fibers and loops (9). The requirement for biologically significant molecules to reach different destinations within the cell nucleus raises the question, how is the diffusive route directed?…”

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“…2A); (ii) pCF(1), correlation of pixels to adjacent pixels in the same DNA density environment (Fig. 2B); (iii) pCF (8), correlation of pixels in low DNA density to pixels in high DNA density (Fig. 2C); (iv) pCF (14), correlation of pixels in low DNA density to distant pixels in low DNA density, separated by a region of high DNA density (as well as pixels in high DNA density to pixels in high DNA density, separated by a region of low DNA density) (Fig.…”

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In vivo pair correlation analysis of EGFP intranuclear diffusion reveals DNA-dependent molecular flow

Hinde

Cardarelli

Digman

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

135

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No methods proposed thus far have the capability to measure overall molecular flow in the nucleus of living cells. Here, we apply the pair correlation function analysis (pCF) to measure molecular anisotropic diffusion in the interphase nucleus of live cells. In the pCF method, we cross-correlate fluctuations at several distances and locations within the nucleus, enabling us to define migration paths and barriers to diffusion. We use monomeric EGFP as a prototypical inert molecule and measure flow in and between different nuclear environments. Our results suggest that there are two disconnect molecular flows throughout the nucleus associated with high and low DNA density regions. We show that different density regions of DNA form a networked channel that allows EGFP to diffuse freely throughout, however with restricted ability to traverse the channel. We also observe rare and sudden bursts of molecules traveling across DNA density regions with characteristic time of ≈300 ms, suggesting intrinsic localized change in chromatin structure. This is a unique in vivo demonstration of the intricate chromatin network showing channel directed diffusion of an inert molecule with high spatial and temporal resolution.chromatin organization | fluctuation spectroscopy | nucleus structure N uclear architecture is fundamental to the manner in which molecules traverse the nucleus (1). The cell nucleus is a functionally and spatially structured organelle (2) in which diffusion is the mode of motion for inert molecules (3-5). The diffusion of molecules within the nucleus is obstructed by the steric constraints imposed by structural components, such as chromatin (6, 7). Proposed models for 3D arrangement of chromatin vary from defined regions of chromatin compartmentalisation (8) to intermingled chromatin fibers and loops (9). The requirement for biologically significant molecules to reach different destinations within the cell nucleus raises the question, how is the diffusive route directed? Given that diffusion cannot be regulated because it is essentially a default mechanism of motion (10), it has been postulated that structural features of the nucleus must impart retention at particular sites and control flux of movement between compartments (1, 11).Insights into intranuclear trafficking are predominantly derived from measurement of the accessibility of the nuclear landscape and the effect it has on diffusion of biologically active and inert molecules. Current approaches commonly used for such investigations are fluorescence recovery after photo bleaching (FRAP) (12, 13), single particle tracking (SPT) (14), and fluorescence correlation spectroscopy (FCS) (15, 16). FRAP, however, is invasive because it requires high illumination power on the sample to induce photobleaching, and SPT requires the observation of isolated particles for a long time, which yields poor statistics. FCS, in contrast, provides information at the single molecule level with good statistics by averaging the behavior of many molecules (10), and this technique ...

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Role of Chromosome Territories in the Functional Compartmentalization of the Cell Nucleus

Cited by 455 publications

References 85 publications

Involvement of in situ conformation of ribosomal genes and selective distribution of upstream binding factor in rRNA transcription.

Involvement of in situ conformation of ribosomal genes and selective distribution of upstream binding factor in rRNA transcription.

Micromechanical studies of mitotic chromosomes

In vivo pair correlation analysis of EGFP intranuclear diffusion reveals DNA-dependent molecular flow

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