Tissue-specific spatial organization of genomes

Background

Genomes are organized in vivo in the form of chromosomes. Each chromosome occupies a distinct nuclear subvolume in the form of a chromosome territory. The spatial positioning of chromosomes within the interphase nucleus is often nonrandom. It is unclear whether the nonrandom spatial arrangement of chromosomes is conserved among tissues or whether spatial genome organization is tissue-specific.

Results

Using two-dimensional and three-dimensional fluorescence in situ hybridization we have carried out a systematic analysis of the spatial positioning of a subset of mouse chromosomes in several tissues. We show that chromosomes exhibit tissue-specific organization. Chromosomes are distributed tissue-specifically with respect to their position relative to the center of the nucleus and also relative to each other. Subsets of chromosomes form distinct types of spatial clusters in different tissues and the relative distance between chromosome pairs varies among tissues. Consistent with the notion that nonrandom spatial proximity is functionally relevant in determining the outcome of chromosome translocation events, we find a correlation between tissue-specific spatial proximity and tissue-specific translocation prevalence.

Conclusions

Our results demonstrate that the spatial organization of genomes is tissue-specific and point to a role for tissue-specific spatial genome organization in the formation of recurrent chromosome arrangements among tissues.

     

Endocardial endothelium in the rat: junctional organization and permeability

Selective permeability of endocardial endothelium has been suggested as a mechanism underlying the modulation of the performance of subjacent myocardium. In this study, we characterized the organization and permeability of junctional complexes in ventricular endocardial endothelium in rat heart. The length of intercellular clefts viewed en face per unit endothelial cell surface area was lower, and intercellular clefts were deeper in endocardial endothelium than in myocardial vascular endothelium, whereas tight junctions had a similar structure in both endothelia. On this basis, endocardia endothelium. might be less permeable than capillary endothelium. However, confocal scanning laser microscopy showed that intravenously injected dextran 10000 coupled to Lucifer Yellow penetrated first the endocardial endothelium and later the myocardial capillary endothelium. Penetration of dextran 10000 in myocardium occurred earlier through subepicardial capillary endothelium than through subendocardial capillary endothelium. Penetration of tracer might thus be influenced by hydrostatic pressure. Dextran of MW 40000 did not diffuse through either endocardial endothelium or capilary endothelium. The ultrastructure of endocardial endothelium may constitute an adaptation to limit diffusion driven by high hydrostatic pressure in the heart. Differences in paracellular diffusion of dextran 10000 between endocardial endothelium and myocardial vessels, may result from differing permeability properties of the endocardium and underlying myocardium.     

Collision induced spatial organization of microtubules

The dynamic behavior of microtubules in solution can be strongly modified by interactions with walls or other structures. We examine here a microtubule growth model where the increase in size of the plus-end is perturbed by collisions with other microtubules. We show that such a simple mechanism of constrained growth can induce ordered structures and patterns from an initially isotropic and homogeneous suspension. We find that microtubules self-organize locally in randomly oriented domains that grow and compete with each other. A weak orientation bias, similar to the one induced by gravity or cellular boundaries is enough to influence the domain growth direction, eventually leading to a macroscopic sample orientation.     

Molecular organization of the canine major histocompatibility complex

The major histocompatibility complex (MHC) is composed of a tightly linked cluster of genes; in dogs, this is referred to as the dog leukocyte antigen (DLA) region. The canine MHC is located on chromosome 12, and several genes within the DLA region have been identified that have significant sequence similarity to their human counterparts. However, in order to characterize other loci in the DLA region, DNA sequencing has begun using a canine bacterial artificial chromosome (BAC) library. Initially 135 BAC clones were isolated from a BAC library using a mixture of human and canine probes. These BAC clones were screened with locus-specific primers in polymerase chain reactions (PCRs). Fifty-six BAC clones were subjected to FingerPrinted Contig (FPC) analysis and several overlapping clones were identified. One BAC clone RP81-231-G24 has been sequenced. Preliminary sequence analysis of this 150 kb clone indicates that it contains the region where the class I and class III regions are joined and encompasses DLA-12a, DLA-53, DLA-12, DLA-64, TNF-alpha, and a canine gene that appears to resemble the HLA class III gene HSPA1A (HSP70-1).     

Endocardial endothelium in the rat: cell shape and organization of the cytoskeleton

The cytoskeleton in endocardial endothelium of rat heart was examined by en face confocal scanning laser microscopy. In the ventricular cavity, endocardial endothelial cells had a polygonal shape and F-actin staining was generally restricted to the peripheral junctional actin band. Central F-actin bundles, or stress fibers, in endocardial endothelial cells were found on the tendon end of papillary muscles, especially in the right ventricle, and frequently in the outflow tract of both ventricles; elsewhere, stress fibers were scarce. Many endocardial endothelial cells were elongated in areas of endothelium with stress fibers, but no correlation was found between cell elongation and the number of stress fibers. An inverse correlation was found between the number of stress fibers and the surface area of endocardial endothelial cells. Shear stress as well as mechanical deformation of the surface of the ventricular wall during the cardiac cycle may affect cell shape and the organization of actin filaments in endocardial endothelial cells. Vimentin in endocardial endothelial cells formed a filamentous network with some distinct cytoplasmic and juxtanuclear vimentin bundles. No perinuclear ring of vimentin filaments was observed in endocardial endothelium. Microtubules in endocardial endothelial cells were, in contrast to endothelial cells of rat aorta, not aligned, less closely packed and originated from randomly distributed centriolar regions. The cytoskeleton has been suggested to play an important role in cellular functions of vascular endothelial cells. Accordingly, differences in the cytoskeletal organization between endocardial and vascular endothelial cells may relate to differences in functional properties.     

The spatial organization of the genome in mammalian cells

A number of recent studies have indicated that the location of a given mammalian chromosome within the interphase nucleus is related to its size, whereas other work has implicated a chromosome's gene density as a factor. Recent investigations of the degree to which an ordered arrangement of mitotic chromosomes on the metaphase plate is inherited and perpetuated during successive cell cycles have also yielded somewhat controversial results. The arrangement of chromosomes in the nucleus also has been investigated by the analysis of chromosomal translocations, with some surprising recent findings.     

Predicting the spatial organization of chromosomes using epigenetic data

Chromosome folding can reinforce the demarcation between euchromatin and heterochromatin. Two new studies show how epigenetic data, including DNA methylation, can accurately predict chromosome folding in three dimensions. Such computational approaches reinforce the idea of a linkage between epigenetically marked chromatin domains and their segregation into distinct compartments at the megabase scale or topological domains at a higher resolution.Please see related articles: http://dx.doi.org/10.1186/s13059-015-0741-y and http://dx.doi.org/10.1186/s13059-015-0740-z     

Some principles of spatial organization in art

Rules of composition in paintings form a rich probe into the principles of perceptual processing that have been discussed for centuries. These principles can be studied by controlled scientific experiments, but an alternative approach is to use the art works themselves as a database for direct analysis. This paper focuses on the analysis of composition in relation to the canvas frame. An underlying principle is the compositional pyramid rising from the bottom of the frame to a center of consciousness high on the midline, which also finds its expression in the configuration of portrait paintings. The analyses presented reveal a dominant positioning principle for one eye in a portrait to lie on the vertical axis with an unbiased accuracy of the order of +/-5%. Analysis of the vertical location shows that the dominant height is at or above the Golden Section level on the vertical axis. In general, the layout of the portrait follows the principle of the compositional pyramid, with a center of consciousness at its apex, but there are many other compositional principles at work in the corpus of portraits in general. Analysis of the portraits of particular artists reveals that special features of their work must be considered in order to identify those that do and do not conform to the eye-centering principle.     

Biotopes and spatial organization of arthropod communities

Plant, spider, beetle, and ground beetle communities were studied in different agrolandscape biotopes (a wheat field, a field margin, and a forest belt) of Krasnodar Territory. In these biotopes, borders between plant communities were distinct. On the contrary, arthropod communities were not usually confined to the certain biotopes. The high degree of mobility of arthropod species resulted in a decrease in their association with the biotope. Representatives of some species (especially, beetles) were revealed in all the biotopes. In relation to season and some other factors, they frequently concentrated in different biotopes. Analysis of arthropod assemblages only within a single biotope gives us a rather impoverished knowledge of the whole population. It is necessary to study these assemblages not only within the basic biotope, but also in adjacent ones.     

Regional characteristics of the organization of the aortic endothelium (a quantitative analysis)

By means of SEM-analysis in 110 microphotos (from 14 aortas of white rats) with the aim to estimate heteromorphism of the thoracic part endothelium, quantitative characteristics of endotheliocytes have been studied in the ventral and dorsal surfaces, and also around the ostia of the intercostal arteries. For the quantitative analysis organization of the lines of the interendotheliocyte borders is taken into account. Endotheliocytes around the ostium are more elongated but occupy less area and have less straight contours in comparison with cells in other regions; they have also greater variability. Essential differences in arranging the endothelial cells into the layer on the ventral and dorsal surfaces of the aorta are revealed.