Published by Oxford University Press 2008.
On the Contribution of Spatial Genome Organization to Cancerous Chromosome Translocations
Affiliation of authors: National Cancer Institute, National Institutes of Health, Bethesda, MD
Correspondence to: Tom Misteli, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 (e-mail: mistelit{at}mail.nih.gov).
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ABSTRACT |
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 Top Abstract IntroductionSpatial Proximity as a...Contact First vs Breakage...A Model for the...References |
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The formation of cancer translocations requires the physical interaction of the translocating chromosomes. It has been postulated that the nonrandom spatial organization of the genome within the cell nucleus contributes to determining the outcome of chromosomal translocation. Comparative analysis of the spatial arrangement of translocations partners and their frequency of translocation suggests that translocations occur preferentially among proximally positioned genome regions. This model makes predictions about mechanisms of translocations and the dynamic properties of genome regions in vivo. Elucidating the contribution of spatial genome organization to the formation of chromosome translocations is an integral part of understanding how translocations form in vivo and has provoked the interrogation of several fundamental aspects of genome cell biology, including tissue-specific differences in genome organization, dynamics of genomes in vivo, and the mechanisms that are determining genome organization in vivo.
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INTRODUCTION |
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TopAbstractIntroductionSpatial Proximity as a...Contact First vs Breakage...A Model for the...References |
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Genomes are nonrandomly arranged within the cell nucleus (1,2). In higher eukaryotes, each chromosome occupies a distinct, spatially limited space within the interphase nucleus, referred to as chromosome territory. The position of each territory within the nuclear space is nonrandom. In human cells, the location of chromosomes has been linked to their gene density with gene-rich chromosomes preferentially located toward the interior of the nucleus, whereas gene-poor chromosomes accumulate at the nuclear periphery (3). Similar preferential localization patterns have been detected for single genes (4). Positioning patterns of chromosomes and genes are tissue- and cell-type specific and can vary according to the proliferation status of cells and the transcriptional activity of genes (5–7). The precise relationship of chromosome and gene position with genome activity is unknown; neither are the molecular mechanisms that give rise to nonrandom positioning patterns.
The nonrandom distribution of chromosomes and genes within the nuclear space inevitably leads to the formation of preferential genome neighborhoods where particular genome regions are in preferential spatial proximity (2,8). A classic example of such spatial neighborhoods is the nucleolus where multiple chromosomes bearing tandem repeats of ribosomal RNA genes cluster to form a distinct nuclear subcompartment.
Similarly, in yeast, tRNA genes cluster near the nucleolus, and in mammalian cells, transcriptionally silent centromere regions cluster in nuclear domains referred to as chromocenters (9).
The nonrandom proximity of genome regions has recently been found to have functional relevance because expression of genes can be regulated via interactions with control regions on different chromosomes (10). Positive or negative regulation occurs via interchromosomal physical interaction between the regulatory element on one chromosome and the target gene on another chromosome. For example, in naive T-helper cells, the TH2 locus control region on mouse chromosome 11 physically interacts with the IFN
locus on chromosome 10 to suppress it. Upon stimulation to differentiate, the two genome regions separate and IFN transcription commences (11). Positive regulation is evident in the olfactory receptor (OR) system where the regulatory region on chromosome 14 interacts selectively with OR genes on several chromosomes to activate them (12). In addition to a role in genome regulation, nonrandom spatial proximity is now also recognized to contribute to determining partners involved in chromosomal translocations (13).
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Spatial Proximity as a Contributor to Translocation Frequency |
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A role for spatial proximity in the formation of chromosomal translocations seems obvious considering that the generation of a chromosomal translocation absolutely requires the physical interaction of the two translocation partners (5,13). Given the nonrandom spatial positioning of genes and chromosomes within the nucleus, the closer two genome regions are on average to each other, the higher is their probability of translocating with each other (Figure 1). The importance of spatial proximity in determining translocation partners is most evident in intrachromosomal rearrangements. In radiation-induced papillary thyroid tumors, the RET gene frequently translocates with the H4 locus that is located more than 30 Mb away on the same chromosome (14). Remarkably, when the position of the loci were mapped by fluorescence in-situ hybridization, they were found to colocalize with high frequency, suggesting that the chromosome is looped to juxtapose the two, potentially facilitating their illegitimate joining when double-strand breaks (DBSs) occur.
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Observations on interchromosomal translocation partners further point to a determining role of nonrandom spatial proximity in the formation of chromosomal translocations. In mice, chromosomes 12, 14, and 15 are found in a prominent spatial cluster in a high fraction of lymphocytes, where they frequently undergo translocations (8). Along the same lines, translocations among human chromosomes 4, 9, 13, and 18 that are preferentially found at the nuclear periphery occur at higher frequencies than with internally localized chromosomes, presumably due to their spatial clustering at the nuclear edge (15). Correlations between spatial proximity and translocation frequency are not limited to entire chromosomes but also apply to specific genes. In humans, several prominent translocation partners including BCR-ABL, PML-RARa, and MYC-IGH are often in preferential spatial proximity (4,16–19). One of the strongest arguments for a role of spatial proximity in translocation formation comes from analysis of Burkitt’s lymphoma rearrangements. In this system, the spatial proximity of MYC relative to its three possible translocation partners IGH, IGK, and IG
directly correlates with the observed frequency in patients (4). Additional support for a role of spatial proximity in formation of translocations comes from comparison of positioning patterns in different tissues. The intrachromosomal translocation partners RET and H4 are only found in spatial proximity in thyroid tissue where they give rise to translocations, but not in mammary tissues where they do not undergo rearrangements (14). In mouse, chromosomes 12 and 15 that are frequently involved in translocations in lymphoma, often pair, but they do not so in hepatocytes where they do not translocate (5). Similarly, chromosomes 5 and 6 that are frequently involved in hepatoma translocations, pair in hepatocytes, but not in lymphocytes (5). It is tempting to speculate that the observed tissue-specific arrangement of chromosomes and genes may contribute to the tissue preference of recurrent translocations.
A contribution of spatial proximity to determining the outcome of chromosomal translocations is also in line with recent insights into the structural organization of chromosomes in the interphase nucleus. Although chromosomes clearly occupy distinct territories, their edges intermingle and chromatin loops from one chromosome invade the territory of its neighbors bringing genomes regions from distinct chromosomes in intimate spatial proximity (20). The intermingling chromatin loops may be more susceptible to DSBs due to their decondensed nature, and the zone between chromosomes territories may be a preferential site of formation of chromosomal translocations among neighboring chromosomes. In support of this possibility, the degree of intermingling between chromosomes strongly correlates with observed translocations frequencies (20).
Although there is growing evidence for a role of spatial proximity in translocation formation, there are several caveats in the experimental data that are worth pointing out. Firstly, most studies are retrospective. The position of genomic regions is analyzed in normal tissues, which are assumed, but not demonstrated, to undergo translocations. Secondly, these studies all use heterogeneous cell populations, and it is not clear in what subpopulation translocations originally form. Similarly, the reported tumor translocations represent a highly selected subpopulation of cells and it is not clear in what cells the translocations originate. On the other hand, the fact that correlations between positioning patterns and translocation frequencies are detected even in these heterogeneous populations strengthens the conclusions. Thirdly, it is clear that the probability of DSB formation differs throughout the genome and that some regions undergo breaks with statistically significant higher frequency than others. The heterogeneity in DSB formation is not taken into account in these analyses. These limitations could be overcome by development of experimental systems in which translocations can be induced in a controlled manner and the fate of the broken chromosomes directly tracked in real time. Such efforts are now underway. For example, induction of a single DSB at a defined location in a Long Interspecsed nuclear element (LINE) element in human chromosomes revealed the preferential recombination of these sites with other LINE elements on the same chromosome and only sporadic recombination with elements on other chromosomes (21).
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Contact First vs Breakage First |
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TopAbstractIntroductionSpatial Proximity as a...Contact First vs Breakage...A Model for the...References |
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Two fundamentally different models for how chromosomal translocations form have been entertained (Figure 2). In the contact-first model, translocations can only occur between DSB that are located in close spatial proximity at the time of breakage. In this model, physical association of translocating regions occurs before DSB formation. On the other hand, in a breakage-first model, translocations occur between DSBs located far apart. In this model, broken chromosome ends undergo large-scale motions to relocalize within the nucleus in search of suitable translocation partners, and physical association between broken chromosome ends on different chromosomes occurs only after chromosomes suffer DSBs.
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The proposal that the spatial proximity of partners influences translocation outcome assumes the contact-first model. If broken chromosomes were able to roam the nucleus freely, the determining role of the spatial position of a broken genome region would likely be neutralized by the positional change of the broken chromosome end. A key question in testing the role of spatial proximity in formation of translocation and in distinguishing between contact-first and breakage-first models is, therefore, whether free DSBs are able to move freely through the nucleus.
It is well established that the motion of the intact chromatin fiber is very limited within the mammalian cell nucleus (22–24). Live cell tracking of fluorescently tagged gene loci reveals that spatially limited constrained diffusional motion of a locus within a radius of 
1 µm. Thus, in an average nucleus of 10µm in diameter, a locus can only explore about 1/125th of the total nuclear volume. Upon induction of large-scale DNA damage by 
-particle irradiation, DSBs have been observed to move over distances of more than 2 µm and to aggregate with each other within 60 minutes (25). On the other hand, induction of large-scale DSBs by soft X-rays or by UV- and -irradiation did not reveal any motion (26,27). Both the observed motion and the absence of motion are difficult to interpret in these experiments as it is not clear how induction of large-scale DNA damage affects the behavior of chromatin and whether these experimental methods may trigger stress responses that might alter the motion of chromatin. Tracking of the movement of broken chromosome ends in living cells showed that cut ends are unable to more over large distances supporting the contact-first model (28).
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A Model for the Formation of Chromosomal Translocations in the Context of Nuclear Architecture |
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TopAbstractIntroductionSpatial Proximity as a...Contact First vs Breakage...A Model for the...References |
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Considering the nonrandom spatial organization of genomes and the evidence for positioning effects, a model for how chromosome translocations occur in vivo emerges. The nonrandom arrangement of chromosomes and genes creates spatial genome neighborhoods in which particular genome regions are preferentially brought together.
The position of these regions does not change as gene loci only undergo constrained local motion. Nearby genome regions on different chromosomes, however, may be in physical contact due to intermingling of chromatin from distinct chromosomes.
Upon formation of DSBs, possibly preferentially in the intermingling regions due to the decondensed nature of the chromatin fiber, broken ends physically interact and they may be illegitimately rejoined to form a translocation. This may occur among DSBs located distally from each other but most likely is favored when breaks occur in close spatial proximity, because in the former case DSBs may be repaired before they find a potential translocation partner. This model provides a rough framework for how translocations form in vivo. It must now be refined by addressing what are the factors that determine the position and the mobility of genome regions in vivo, and what the kinetics of finding a translocation partner and of formation of the actual translocation are. The answers to these questions will go a long way toward understanding the cell biology of translocations.
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