The 4D Nucleome: Genome Compartmentalization in an Evolutionary Context.

4D nucleome research aims to understand the impact of nuclear organization in space and time on nuclear functions, such as gene expression patterns, chromatin replication, and the maintenance of genome integrity. In this review we describe evidence that the origin of 4D genome compartmentalization can be traced back to the prokaryotic world. In cell nuclei of animals and plants chromosomes occupy distinct territories, built up from ~1 Mb chromatin domains, which in turn are composed of smaller chromatin subdomains and also form larger chromatin domain clusters. Microscopic evidence for this higher order chromatin landscape was strengthened by chromosome conformation capture studies, in particular Hi-C. This approach demonstrated ~1 Mb sized, topologically associating domains in mammalian cell nuclei separated by boundaries. Mutations, which destroy boundaries, can result in developmental disorders and cancer. Nucleosomes appeared first as tetramers in the Archaea kingdom and later evolved to octamers built up each from two H2A, two H2B, two H3, and two H4 proteins. Notably, nucleosomes were lost during the evolution of the Dinoflagellata phylum. Dinoflagellate chromosomes remain condensed during the entire cell cycle, but their chromosome architecture differs radically from the architecture of other eukaryotes. In summary, the conservation of fundamental features of higher order chromatin arrangements throughout the evolution of metazoan animals suggests the existence of conserved, but still unknown mechanism(s) controlling this architecture. Notwithstanding this conservation, a comparison of metazoans and protists also demonstrates species-specific structural and functional features of nuclear organization.

[Stress echocardiography and its central role in cardiac diagnostics]. / Stressechokardiographie und ihre zentrale Rolle in der kardiologischen Diagnostik.

Stress echocardiography (SE) has an established central role as a diagnostic tool in cardiology. It is not only an established method for the diagnostic and prognostic stratification of patients with coronary artery disease but also shows an emerging value for assessment of cardiac function beyond coronary artery disease. The enormous conceptual technological development of ultrasound technology (Doppler, digitizing, tissue Doppler imaging, strain technology, 3­D-echo and new ultrasound contrast agents) has led to applications of SE in almost all diagnostic fields of cardiology. The use of SE provides not only the possibility to identify coronary stenosis but also to evaluate the function of the microvasculature and heart valves, to detect possible pulmonary hypertension and also to test the systolic/diastolic reaction/mechanics of the right/left ventricle (LV/RV) and left atrium (LA) in response to load. Further developments of ultrasound technology enable better temporal resolution and contemporary analyses of cardiac mechanics of the LV/RV and LA. Pharmacological stress echocardiography extends the diagnostic field to patients who are not able to endure physical stress. SE represents an environmentally friendly, patient-friendly, cost-efficient and radiation-free examination method; however, SE requires extensive basic training as well as continuous training of the examiner to ensure that all possible advantages of the method can be utilized to the benefit of patients.

Comparative chromosome painting discloses homologous segments in distantly related mammals.

Comparative chromosome painting, termed ZOO-FISH, using DNA libraries from flow sorted human chromosomes 1, 16, 17 and X, and mouse chromosome 11 discloses the presence of syntenic groups in distantly related mammalian orders ranging from primates (Homo sapiens), rodents (Mus musculus), even-toed ungulates (Muntiacus muntjak vaginalis and Muntiacus reevesi) and whales (Balaenoptera physalus). These mammalian orders have evolved separately for 55-80 million years (Myr). We conclude that ZOO-FISH can be used to generate comparative chromosome maps of a large number of mammalian species.

Interfaces of ionic liquids and transition metal surfaces-adsorption, growth, and thermal reactions of ultrathin [C1C1Im][Tf2N] films on metallic and oxidised Ni(111) surfaces.

Ultrathin films of the ionic liquid 1,3-dimethylimidazolium bis(trifluoromethylsulfonyl)imide ([C(1)C(1)Im][Tf(2)N]) were deposited on differently terminated Ni(111) single crystal surfaces. The initial wetting behaviour, the growth characteristics, the molecular arrangement at the interface, and thermal reactivity were investigated using angle-resolved X-ray photoelectron spectroscopy (ARXPS). On clean Ni(111), the initial growth occurs in a layer-by-layer mode. At submonolayer coverages up to at least 0.40 ML, a preferential arrangement of the IL ions in a bilayer structure, with the imidazolium cations in contact with the Ni surface atoms and the anions on top of the cation, is deduced. For higher coverages, a transition to a checkerboard-type arrangement occurs, which is most likely due to repulsive dipole-dipole interactions in the first layer. An overall preference for a checkerboard-type adsorption behaviour, i.e., anions and cations adsorbing next to each other, is found on the oxygen-precovered O(√3×√3)R30° Ni(111) surface. The thermal stability of adsorbed IL layers on Ni(111) and on a fully oxidised Ni(111) surface was studied by heating the layers to elevated temperatures. For clean Ni(111) reversible adsorption takes place. For the oxidised surface, however, only cation-related moieties desorb, starting at ~450 K, while anion-related signals remain on the surface up to much higher temperatures.

Liquid/solid interface of ultrathin ionic liquid films: [C1C1Im][Tf2N] and [C8C1Im][Tf2N] on Au(111).

Ultrathin films of two imidazolium-based ionic liquids (IL), [C(1)C(1)Im][Tf(2)N] (= 1,3-dimethylimidazolium bis(trifluoromethyl)imide) and [C(8)C(1)Im][Tf(2)N] (= 1-methyl-3-octylimidazolium bis(trifluoromethyl)imide) were prepared on a Au(111) single-crystal surface by physical vapor deposition in ultrahigh vacuum. The adsorption behavior, orientation, and growth were monitored via angle-resolved X-ray photoelectron spectroscopy (ARXPS). Coverage-dependent chemical shifts of the IL-derived core levels indicate that for both ILs the first layer is formed from anions and cations directly in contact with the Au surface in a checkerboard arrangement and that for [C(8)C(1)Im][Tf(2)N] a reorientation of the alkyl chain with increasing coverage is found. For both ILs, geometry models of the first adsorption layer are proposed. For higher coverages, both ILs grow in a layer-by-layer fashion up to thicknesses of at least 9 nm (>10 ML). Moreover, beam damage effects are discussed, which are mainly related to the decomposition of [Tf(2)N](-) anions directly adsorbed at the gold surface.

Insights into the surface composition and enrichment effects of ionic liquids and ionic liquid mixtures.

A systematic study of ionic liquid surfaces by angle resolved X-ray photoelectron spectroscopy (ARXPS) is presented. By reviewing recent and presenting new results for imidazolium-based ionic liquids (ILs), we discuss the impact of chemical differences on surface composition and on surface enrichment effects. (1) For the hydrophilic ethylene glycol (EG) functionalised ILs [Me(EG)MIm][Tf(2)N], [Et(EG)(2)MIm][Tf(2)N] and [Me(EG)(3)MIm][Tf(2)N], which vary in the number of ethylene glycol units (from 1 to 3), we find that the surface composition of the near-surface region is in excellent agreement with the bulk composition, which is attributed to attractive interactions between the oxygen atoms on the cation to the hydrogen atoms on the imidazolium ring. (2) For [C(n)C(1)Im][Tf(2)N] (where n = 1-16), i.e. ILs with an alkyl chain of increasing length, an enrichment of the aliphatic carbons is observed for longer chains (n > 2), at the expense of the polar cation head groups and the anions in the first molecular layer, both of which are located approximately at the same distance from the outer surface. (3) To study the influence of the anion on the surface enrichment, we investigated ten ILs [C(8)C(1)Im][X] with the same cation, but very different anions [X](-). In all cases, surface enrichment of the cation alkyl chains is found, with the degree of enrichment decreasing with increasing size of the anion, i.e., it is most pronounced for the smallest anions and least pronounced for the largest anions. (4) For the IL mixture [C(2)C(1)Im][Tf(2)N] and [C(12)C(1)Im][Tf(2)N] we find a homogeneous distribution in the outermost surface region with no specific enrichment of the [C(12)C(1)Im](+) cation.

A technical note on quantum dots for multi-color fluorescence in situ hybridization.

Quantum dots (Qdots) are semiconductor nanocrystals, which are photo-stable, show bright fluorescence with narrow, symmetric emission spectra and are available in multiple resolvable colors. We established a FISH protocol for the simultaneous visualization of up to 6 different DNA probes differentially labeled with Qdots and with conventional organic fluorochromes. Using a Leica SP5 laser scanning confocal microscope for image capture, we tested various combinations of hapten-labeled probes detected with streptavidin-Qdot525, sheep anti-digoxigenin-Qdot605, rat anti-dinitrophenyl-Qdot655 and goat anti-mouse-Qdot655, respectively, together with FITC-dUTP-, Cy3-dUTP- and Texas Red-dUTP-labeled probes. We further demonstrate that Qdots are suitable for imaging of FISH probes using 4Pi microscopy, which promises to push the resolution limits of light microscopy to 100 nanometers or less when applying a deconvolution algorithm, but requires the use of highly photo-stable fluors.

Rad51 accumulation at sites of DNA damage and in postreplicative chromatin.

Rad51, a eukaryotic RecA homologue, plays a central role in homologous recombinational repair of DNA double-strand breaks (DSBs) in yeast and is conserved from yeast to human. Rad51 shows punctuate nuclear localization in human cells, called Rad51 foci, typically during the S phase (Tashiro, S., N. Kotomura, A. Shinohara, K. Tanaka, K. Ueda, and N. Kamada. 1996. Oncogene. 12:2165-2170). However, the topological relationships that exist in human S phase nuclei between Rad51 foci and damaged chromatin have not been studied thus far. Here, we report on ultraviolet microirradiation experiments of small nuclear areas and on whole cell ultraviolet C (UVC) irradiation experiments performed with a human fibroblast cell line. Before UV irradiation, nuclear DNA was sensitized by the incorporation of halogenated thymidine analogues. These experiments demonstrate the redistribution of Rad51 to the selectively damaged, labeled chromatin. Rad51 recruitment takes place from Rad51 foci scattered throughout the nucleus of nonirradiated cells in S phase. We also demonstrate the preferential association of Rad51 foci with postreplicative chromatin in contrast to replicating chromatin using a double labeling procedure with halogenated thymidine analogues. This finding supports a role of Rad51 in recombinational repair processes of DNA damage present in postreplicative chromatin.

Centromere and telomere movements during early meiotic prophase of mouse and man are associated with the onset of chromosome pairing.

The preconditions and early steps of meiotic chromosome pairing were studied by fluorescence in situ hybridization (FISH) with chromosome-specific DNA probes to mouse and human testis tissue sections. Premeiotic pairing of homologous chromosomes was not detected in spermatogonia of the two species. FISH with centromere- and telomere-specific DNA probes in combination with immunostaining (IS) of synaptonemal complex (SC) proteins to testis sections of prepuberal mice at days 4-12 post partum was performed to study sequentially the meiotic pairing process. Movements of centromeres and then telomeres to the nuclear envelope, and of telomeres along the nuclear envelope leading to the formation of a chromosomal bouquet were detected during mouse prophase. At the bouquet stage, pairing of a mouse chromosome-8-specific probe was observed. SC-IS and simultaneous telomere FISH revealed that axial element proteins appear as large aggregates in mouse meiocytes when telomeres are attached to the nuclear envelope. Axial element formation initiates during tight telomere clustering and transverse filament-IS indicated the initiation of synapsis during this stage. Comparison of telomere and centromere distribution patterns of mouse and human meiocytes revealed movements of centromeres and then telomeres to the nuclear envelope and subsequent bouquet formation as conserved motifs of the pairing process. Chromosome painting in human spermatogonia revealed compacted, largely mutually exclusive chromosome territories. The territories developed into long, thin threads at the onset of meiotic prophase. Based on these results a unified model of the pairing process is proposed.

Three-dimensional reconstruction of painted human interphase chromosomes: active and inactive X chromosome territories have similar volumes but differ in shape and surface structure.

This study provides a three-dimensional (3D) analysis of differences between the 3D morphology of active and inactive human X interphase chromosomes (Xa and Xi territories). Chromosome territories were painted in formaldehyde-fixed, three-dimensionally intact human diploid female amniotic fluid cell nuclei (46, XX) with X-specific whole chromosome compositive probes. The colocalization of a 4,6-diamidino-2-phenylindole dihydrochloride-stained Barr body with one of the two painted X territories allowed the unequivocal discrimination of the inactive X from its active counterpart. Light optical serial sections were obtained with a confocal laser scanning microscope. 3D-reconstructed Xa territories revealed a flatter shape and exhibited a larger and more irregular surface when compared to the apparently smoother surface and rounder shape of Xi territories. The relationship between territory surface and volume was quantified by the determination of a dimensionless roundness factor (RF). RF and surface area measurements showed a highly significant difference between Xa and Xi territories (P < 0.001) in contrast to volume differences (P > 0.1). For comparison with an autosome of similar DNA content, chromosome 7 territories were additionally painted. The 3D morphology of the chromosome 7 territories was similar to the Xa territory but differed strongly from the Xi territory with respect to RF and surface area (P < 0.001).

Dynamics of DNA replication factories in living cells.

DNA replication occurs in microscopically visible complexes at discrete sites (replication foci) in the nucleus. These foci consist of DNA associated with replication machineries, i.e., large protein complexes involved in DNA replication. To study the dynamics of these nuclear replication foci in living cells, we fused proliferating cell nuclear antigen (PCNA), a central component of the replication machinery, with the green fluorescent protein (GFP). Imaging of stable cell lines expressing low levels of GFP-PCNA showed that replication foci are heterogeneous in size and lifetime. Time-lapse studies revealed that replication foci clearly differ from nuclear speckles and coiled bodies as they neither show directional movements, nor do they seem to merge or divide. These four dimensional analyses suggested that replication factories are stably anchored in the nucleus and that changes in the pattern occur through gradual, coordinated, but asynchronous, assembly and disassembly throughout S phase.

Active and inactive genes localize preferentially in the periphery of chromosome territories.

The intranuclear position of a set of genes was analyzed with respect to the territories occupied by the whole chromosomes in which these genes are localized. Genes and their respective chromosome territories were simultaneously visualized in three-dimensionally preserved nuclei applying dual color fluorescence in situ hybridization. Three coding (DMD, MYH7, and HBB) and two noncoding sequences (D1Z2 and an anonymous sequence) were analyzed in four different cell types, including cells where DMD and MYH7 are actively transcribed. Spatial analysis by confocal laser scanning microscopy revealed that the genes are preferentially located in the periphery of chromosome territories. This positioning was independent from the activity of the genes. In contrast, the non-expressed anonymous fragment was found randomly distributed or localized preferentially in the interior of the corresponding chromosome territory. Furthermore, the distribution of the analyzed genes within the territorial peripheries was found to be highly characteristic for each gene, and, again, independent from its expression. The impact of these findings with regard to the three-dimensional arrangement of the linear DNA string within chromosome territories, as well as with respect to a putative nuclear subcompartment confining gene expression, are discussed.

Nuclear organization of mammalian genomes. Polar chromosome territories build up functionally distinct higher order compartments.

We investigated the nuclear higher order compartmentalization of chromatin according to its replication timing (Ferreira et al. 1997) and the relations of this compartmentalization to chromosome structure and the spatial organization of transcription. Our aim was to provide a comprehensive and integrated view on the relations between chromosome structure and functional nuclear architecture. Using different mammalian cell types, we show that distinct higher order compartments whose DNA displays a specific replication timing are stably maintained during all interphase stages. The organizational principle is clonally inherited. We directly demonstrate the presence of polar chromosome territories that align to build up higher order compartments, as previously suggested (Ferreira et al. 1997). Polar chromosome territories display a specific orientation of early and late replicating subregions that correspond to R- or G/C-bands of mitotic chromosomes. Higher order compartments containing G/C-bands replicating during the second half of the S phase display no transcriptional activity detectable by BrUTP pulse labeling and show no evidence of transcriptional competence. Transcriptionally competent and active chromatin is confined to a coherent compartment within the nuclear interior that comprises early replicating R-band sequences. As a whole, the data provide an integrated view on chromosome structure, nuclear higher order compartmentalization, and their relation to the spatial organization of functional nuclear processes.

Influence of different substituents on the surface composition of ionic liquids studied using ARXPS.

Angle resolved X-ray photoelectron spectroscopy has been used to study the surface composition of various nonfunctionalized and functionalized 1,3-dialkylimidazolium ionic liquids. For [CnC1Im][Tf2N] (where n = 2-16), an enrichment of the aliphatic carbon was observed for longer chains (n > or = 4). Enrichment of the aliphatic carbon also occurs for alkyl chains attached to the anion, as observed for [C2C1Im][OcOSO3]. Oligo(ethyleneglycol)ether (PEG) functionalities in the cation lead to a surface composition close to bulk stoichiometry and thus a loss in enrichment of the chains. This effect is attributed to attractive interactions between the oxygen atoms on the cation to the hydrogen atoms on the imidazolium ring for [Et(EG)2MIm] [Tf2N] and [Me(EG)3MIm][Tf2N].

Influence of different anions on the surface composition of ionic liquids studied using ARXPS.

Angle-resolved X-ray photoelectron spectroscopy has been used to study the influence of different types of anions on the surface composition of ionic liquids (ILs). We have investigated nine ILs with the same cation, 1-octyl-3-methylimidazolium [C(8)C(1)Im](+), but very different anions. In all cases, an enrichment of the cation alkyl chains is found at the expense of the polar cation head groups and the anions in the first molecular layer. This enhancement effect decreases with increasing size of the anion, which means it is most pronounced for the smallest anions and least pronounced for the largest anions. A simple model is proposed to explain the experimental observations.

Chromosome shattering: a mitotic catastrophe due to chromosome condensation failure.

Chromosome shattering has been described as a special form of mitotic catastrophe, which occurs in cells with unrepaired DNA damage. The shattered chromosome phenotype was detected after application of a methanol/acetic acid (MAA) fixation protocol routinely used for the preparation of metaphase spreads. The corresponding phenotype in the living cell and the mechanism leading to this mitotic catastrophe have remained speculative so far. In the present study, we used V79 Chinese hamster cells, stably transfected with histone H2BmRFP for live-cell observations, and induced generalized chromosome shattering (GCS) by the synergistic effect of UV irradiation and caffeine posttreatment. We demonstrate that GCS can be derived from abnormal mitotic cells with a parachute-like chromatin configuration (PALCC) consisting of a bulky chromatin mass and extended chromatin fibers that tether centromeres at a remote, yet normally shaped spindle apparatus. This result hints at a chromosome condensation failure, yielding a "shattered" chromosome complement after MAA fixation. Live mitotic cells with PALCCs proceeded to interphase within a period similar to normal mitotic cells but did not divide. Instead they formed cells with highly abnormal nuclear configurations subject to apoptosis after several hours. We propose a factor depletion model where a limited pool of proteins is involved both in DNA repair and chromatin condensation. Chromosome condensation failure occurs when this pool becomes depleted.

Nonrigid registration of 3-d multichannel microscopy images of cell nuclei.

We present an intensity-based nonrigid registration approach for the normalization of 3-D multichannel microscopy images of cell nuclei. A main problem with cell nuclei images is that the intensity structure of different nuclei differs very much; thus, an intensity-based registration scheme cannot be used directly. Instead, we first perform a segmentation of the images from the cell nucleus channel, smooth the resulting images by a Gaussian filter, and then apply an intensity-based registration algorithm. The obtained transformation is applied to the images from the nucleus channel as well as to the images from the other channels. To improve the convergence rate of the algorithm, we propose an adaptive step length optimization scheme and also employ a multiresolution scheme. Our approach has been successfully applied using 2-D cell-like synthetic images, 3-D phantom images as well as 3-D multichannel microscopy images representing different chromosome territories and gene regions. We also describe an extension of our approach, which is applied for the registration of 3D + t (4-D) image series of moving cell nuclei.

Cell nucleus: chromosome dynamics in nuclei of living cells.

Unraveling chromosome movements in vivo is indispensable for understanding the functional architecture of the nucleus and its relationship to the functional state of the cell. New experimental approaches have now made it possible to monitor chromosome dynamics within the nuclei of living cells.

Transition from initiation to promoter proximal pausing requires the CTD of RNA polymerase II.

The C-terminal domain (CTD) of mammalian RNA polymerase II consists of 52 repeats of the consensus hepta-peptide YSPTSPS, and links transcription to the processing of pre-mRNA. Although Pol II with a CTD shortened to five repeats (Pol II Delta5) is transcriptionally inactive on chromatin templates, it is not clear whether CTD is required for promoter recognition in vivo. Here, we demonstrate that in the context of chromatin, Pol II Delta5 can bind to the c-myc promoter with the same efficiency as wild type Pol II. However, Pol II Delta5 does not form a stable initiation complex, and does not transcribe promoter proximal sequences. Fluorescence recovery after photobleaching (FRAP) experiments with cells expressing enhanced green fluorescent protein (EGFP)-tagged Delta5 or wildtype Pol II revealed a single, highly mobile Pol II Delta5 fraction whereas wildtype Pol II yielded less mobile fractions. These data suggest that CTD is not required for promoter recognition, but rather for subsequent formation of a stable initiation complex and isomerization to an elongation competent complex.

Towards many colors in FISH on 3D-preserved interphase nuclei.

The article reviews the existing methods of multicolor FISH on nuclear targets, first of all, interphase chromosomes. FISH proper and image acquisition are considered as two related components of a single process. We discuss (1) M-FISH (combinatorial labeling + deconvolution + wide-field microscopy); (2) multicolor labeling + SIM (structured illumination microscopy); (3) the standard approach to multicolor FISH + CLSM (confocal laser scanning microscopy; one fluorochrome - one color channel); (4) combinatorial labeling + CLSM; (5) non-combinatorial labeling + CLSM + linear unmixing. Two related issues, deconvolution of images acquired with CLSM and correction of data for chromatic Z-shift, are also discussed. All methods are illustrated with practical examples. Finally, several rules of thumb helping to choose an optimal labeling + microscopy combination for the planned experiment are suggested.