Genome function in higher eukaryotes involves major changes in the spatial organization of the chromatin fiber. Nevertheless, our understanding of chromatin folding is remarkably limited. Polymer models have been used to describe chromatin folding. However, none of the proposed models gives a satisfactory explanation of experimental data. In particularly, they ignore that each chromosome occupies a confined space, i.e., the chromosome territory. Here, we present a polymer model that is able to describe key properties of chromatin over length scales ranging from 0.5 to 75 Mb. This random loop (RL) model assumes a self-avoiding random walk folding of the polymer backbone and defines a probability P for 2 monomers to interact, creating loops of a broad size range. Model predictions are compared with systematic measurements of chromatin folding of the q-arms of chromosomes 1 and 11. The RL model can explain our observed data and suggests that on the tens-of-megabases length scale P is small, i.e., 10 -30 loops per 100 Mb. This is sufficient to enforce folding inside the confined space of a chromosome territory. On the 0.5-to 3-Mb length scale chromatin compaction differs in different subchromosomal domains. This aspect of chromatin structure is incorporated in the RL model by introducing heterogeneity along the fiber contour length due to different local looping probabilities. The RL model creates a quantitative and predictive framework for the identification of nuclear components that are responsible for chromatin-chromatin interactions and determine the 3-dimensional organization of the chromatin fiber.genome organization ͉ polymer model ͉ chromatin folding T he chromatin fiber inside the interphase nucleus of higher eukaryotes is folded and compacted on several length scales. On the smallest scale the basic filament is formed by wrapping double-stranded DNA around a histone protein octamer, forming a nucleosomal unit every Ϸ200 bp. This beads-on-a-string type filament in turn condenses to a fiber of 30-nm diameter, which detailed organization is still under debate (1-3). At bigger length scales the spatial organization of chromatin in the interphase nucleus is even more unclear. Imaging techniques do not allow one to directly follow the folding path of the chromatin fiber in the interphase nucleus. Therefore, indirect approaches have been used to obtain information about chromatin folding. One way, pursued in this study, is fluorescence in situ hybridization (FISH) to measure the relationship between the physical distance between genomic sequence elements (in m) and their genomic distance (in megabases). There have been several attempts to explain the folding of chromatin in the interphase nucleus using polymer models. The strength of polymer models is their ability to make predictions on the structure of chromatin by pointing out the driving forces for observed folding motifs. These predictions can then be tested experimentally. However, a polymer model that is able to explain chromatin folding spanning differen...

The three-dimensional (3D) organization of the chromosomal fiber in the human interphase nucleus is an important but poorly understood aspect of gene regulation. Here we quantitatively analyze and compare the 3D structures of two types of genomic domains as defined by the human transcriptome map. While ridges are gene dense and show high expression levels, antiridges, on the other hand, are gene poor and carry genes that are expressed at low levels. We show that ridges are in general less condensed, more irregularly shaped, and located more closely to the nuclear center than antiridges. Six human cell lines that display different gene expression patterns and karyotypes share these structural parameters of chromatin. This shows that the chromatin structures of these two types of genomic domains are largely independent of tissue-specific variations in gene expression and differentiation state. Moreover, we show that there is remarkably little intermingling of chromatin from different parts of the same chromosome in a chromosome territory, neither from adjacent nor from distant parts. This suggests that the chromosomal fiber has a compact structure that sterically suppresses intermingling. Together, our results reveal novel general aspects of 3D chromosome architecture that are related to genome structure and function.

Changes in chromatin structure are a key aspect in the epigenetic regulation of gene expression. We have used a lac operator array system to visualize by light microscopy the effect of heterochromatin protein 1 (HP1) ␣ (HP1␣) and HP1␤ on large-scale chromatin structure in living mammalian cells. The structure of HP1, containing a chromodomain, a chromoshadow domain, and a hinge domain, allows it to bind to a variety of proteins. In vivo targeting of an enhanced green fluorescent protein-tagged HP1-lac repressor fusion to a lac operator-containing, gene-amplified chromosome region causes local condensation of the higher-order chromatin structure, recruitment of the histone methyltransferase SETDB1, and enhanced trimethylation of histone H3 lysine 9. Polycomb group proteins of both the HPC/HPH and the EED/EZH2 complexes, which are involved in the heritable repression of gene activity, are not recruited to the amplified chromosome region by HP1␣ and HP1␤ in vivo targeting. HP1␣ targeting causes the recruitment of endogenous HP1␤ to the chromatin region and vice versa, indicating a direct interaction between the two HP1 homologous proteins. Our findings indicate that HP1␣ and HP1␤ targeting is sufficient to induce heterochromatin formation.Packing of the eukaryotic genome into higher-order chromatin structures is tightly related to gene expression (reviewed in references 17 and 37). Changes in chromatin structure are a key element in epigenetic gene control. Transcriptional activation is associated with large-scale chromatin decondensation, whereas silencing is related to condensation (2, 31, 36, 51, 52). The molecular mechanisms that establish and maintain functionally distinct higher-order chromatin states in the interphase nucleus are poorly understood (8,42). Posttranslational modifications of histones have been directly linked with transcriptional regulation and with changes in chromatin structure (reviewed in references 22 and 24). Such modifications alter the interactions between histones and DNA and between chromatin-associated proteins. The "histone code" apparently defines functionally distinct chromatin domains of different transcriptional states (15,21,35,49). Many key questions concerning the role of histone modifications regulating chromatin structure and gene expression are unsolved.A number of heterochromatin-associated proteins, including heterochromatin protein 1 (HP1) and polycomb group (PcG) proteins, which all are involved in epigenetic silencing, share a common evolutionarily conserved domain, the chromodomain (CD), which is responsible for the association with chromatin (4,9,19,24,48). HP1 also contains a chromoshadow domain (CSD), which mediates protein-protein interactions, including homodimerization (1). Moreover, HP1 also binds to DNA and linker histones through its hinge domain (HD), positioned between the CD and the CSD. This HD may also be involved in targeting HP1 to heterochromatin through an RNA binding activity (30). A link between histone modifications and the formation of a repres...

This paper introduces GraphSplatting, a technique which transforms a graph into a two-dimensional scalar field. The scalar field can be rendered as a color coded map, a height field, or a set of contours. Splat fields allow for the visualization of arbitrarily large graphs without cluttering. They provide density information which can be used to determine the structure of the graph. The construction, visualization and interaction with splat fields is discussed. Two applications illustrate to usage of GraphSplatting.

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