RNF26 binds perinuclear vimentin filaments to integrate ER and endolysosomal responses to proteotoxic stress

Proteotoxic stress causes profound endoplasmic reticulum (ER) membrane remodeling into a perinuclear quality control compartment (ERQC) for the degradation of misfolded proteins. Subsequent return to homeostasis involves clearance of the ERQC by endolysosomes. However, the factors that control perinuclear ER integrity and dynamics remain unclear. Here, we identify vimentin intermediate filaments as perinuclear anchors for the ER and endolysosomes. We show that perinuclear vimentin filaments engage the ER-embedded RING finger protein 26 (RNF26) at the C-terminus of its RING domain. This restricts RNF26 to perinuclear ER subdomains and enables the corresponding spatial retention of endolysosomes through RNF26-mediated membrane contact sites (MCS). We find that both RNF26 and vimentin are required for the perinuclear coalescence of the ERQC and its juxtaposition with proteolytic compartments, which facilitates efficient recovery from ER stress via the Sec62-mediated ER-phagy pathway. Collectively, our findings reveal a scaffolding mechanism that underpins the spatiotemporal integration of organelles during cellular proteostasis.

The journey of Ca2+ through the cell - pulsing through the network of ER membrane contact sites

Calcium is the third most abundant metal on earth, and the fundaments of its homeostasis date back to pre-eukaryotic life forms. In higher organisms, Ca²⁺ serves as a cofactor for a wide array of (enzymatic) interactions in diverse cellular contexts and constitutes the most important signaling entity in excitable cells. To enable responsive behavior, cytosolic Ca²⁺ concentrations are kept low through sequestration into organellar stores, particularly the endoplasmic reticulum (ER), but also mitochondria and lysosomes. Specific triggers are then used to instigate a local release of Ca²⁺ on demand. Here, communication between organelles comes into play, which is accomplished through intimate yet dynamic contacts, termed membrane contact sites (MCSs). The field of MCS biology in relation to cellular Ca²⁺ homeostasis has exploded in recent years. Taking advantage of this new wealth of knowledge, in this Review, we invite the reader on a journey of Ca²⁺ flux through the ER and its associated MCSs. New mechanistic insights and technological advances inform the narrative on Ca²⁺ acquisition and mobilization at these sites of communication between organelles, and guide the discussion of their consequences for cellular physiology.

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.

82 STRUCTURAL REMODELLING OF THE NUCLEAR ENVELOPE IN BOVINE PRE-IMPLANTATION EMBRYOS

In the present study, we investigated the changes of the nuclear envelope and its underlying lamina, as well as features of higher order chromatin organisation in bovine embryos generated by in vitro fertilization during pre-implantation development. We used super-resolution, 3-dimensional structured illumination microscopy combined with 2-colour immunostaining of the nucleoporin Nup153 and lamin B serving as markers for nuclear pore complexes (NPC) and the nuclear lamina, respectively. DNA was counterstained with 4′,6-diamidino-2-phenylindole (DAPI). We examined 20 nuclei for the zygote (10 male pronuclei and 10 female pronuclei; n = 10) and the blastocyst (10 trophectoderm and 10 inner cell mass nuclei; n = 1) stage, and 10 nuclei for each the 2-cell (n = 5), 4-cell (n = 3), 8-cell (n = 2), 19-cell (n = 1), and morula (n = 1) stages. We report 4 major findings: (1) At the onset of major genome activation (MGA) nuclei showed a peripheral location of chromosome territories (CT), separated by wide IC channels and surrounding a major lacuna depleted of chromatin. The NPC were exclusively present at sites where DAPI-stained DNA contacted the nuclear lamina, whereas extended lamina regions without such contacts lacked NPC. In post-MGA nuclei, the CT formed a higher order chromatin network distributed throughout the entire nuclear space and the major lacuna disappeared. In line with a switch to a ubiquitous lining of DNA at the lamina, NPC were also uniformly distributed throughout the entire nuclear envelope. These findings shed new light on the conditions that control the integration of NPC into the nuclear envelope. (2) The switch from maternal to embryonic production of mRNA was accompanied by an increased amount of nuclear lamina invaginations covered with NPC, which may serve the increased demands of mRNA export and protein import. (3) Other invaginations, as well as interior nuclear segments and vesicles without contact to the nuclear envelope, were exclusively positive for lamin B. Because an increase in these lamin B positive structures occurred in concert with a massive nuclear volume reduction, we suggest that they reflect a mechanism for fitting the nuclear envelope and its lamina to a shrinking nuclear size throughout bovine pre-implantation development. (4) Throughout the cytoplasm, randomly distributed extranuclear clusters of Nup153 without associated lamin B were frequently observed from the zygote stage up to MGA. These clusters may represent a deposit of maternal Nup153 and likely other nucleoporines not studied here. Corresponding RNA-Seq data revealed deposits of spliced, maternally provided NUP153 mRNA and little unspliced RNA before MGA, which increased strongly at the initiation of embryonic NUP153 expression at MGA. After MGA, these clusters were exclusively located at or near the nuclear border and were no longer present at the morula stage and later. In conclusion, our findings demonstrate the dynamic adaptation of the nuclear envelope to the special needs of bovine pre-implantation development and show the necessity of chromatin association for the integration of nuclear pores into the nuclear envelope.

92 NUCLEAR INVAGINATIONS ADAPT TO RABBIT EARLY EMBRYONIC DEVELOPMENT

Nuclear invaginations carrying nuclear pores may facilitate increased mRNA export and protein import to areas inside the nucleus remote from the nuclear border. In this study on rabbit embryos, we investigated whether large early embryonic nuclei and the increased import/export demands around major embryonic genome activation (MGA) at the 8-cell stage affected the quantity of nuclear invaginations carrying nuclear pores. To achieve this objective, we used super-resolution 3-dimensional structured illumination microscopy on 10 pronuclei or nuclei per stage of 23 in vivo-fertilized and in vitro-cultured embryos stained with antibodies for the nucleoporin NUP153 and lamin B and stained with 4′,6-diamidino-2-phenylindole (DAPI) for chromatin. Statistical comparisons between stages were performed using the Wilcoxon rank-sum test. At the zygote stage, the female pronucleus displayed on average 16.5 and the male pronucleus featured on average 15.25 wide and narrow nuclear envelope invaginations, carrying large or tiny amounts of cytoplasm. Subsequent stages showed predominantly wide invaginations targeting nucleoli. The contact areas between nucleoli and invaginations were free of nuclear pores. In contrast, narrow invaginations, which are the almost exclusive type of invaginations during cattle and mouse pre-implantation development, were not in contact with nucleoli. At the 2-cell stage, the number of invaginations increased to an average of 27.3 invaginations per nucleus (P < 0.05) and increased again to peak at the 4-cell stage with 51.2 invaginations per nucleus (P < 0.01). At the 8-cell stage (MGA), the amount of nuclear invaginations was reduced to 25.4 invaginations per nucleus (P < 0.01). The reduced number of nuclear invaginations at the 8-cell stage could be associated with a significant decrease in average nuclear volume from 2593 µm3 at the 4-cell stage to 960 µm3 at the 8-cell stage (P < 0.001) and a subsequent reduced average distance from areas inside the nucleus to the nuclear border. Nuclear invagination numbers continued their decline at the 21-cell stage with 5.2 invaginations per nucleus (P < 0.001), whereas nuclear volumes decreased to 618 µm3 (P < 0.001). The morula stage, with 6.9 invaginations per nucleus (P = 0.9), and the blastocyst stage, with 4.5 invaginations per nucleus (P = 0.5), showed no more significant changes. Large NUP153 cytoplasmic clusters present before MGA may represent a maternally provided NUP153 deposit. MGA may mark the switch from the use of a NUP153 deposit to on-demand production. Additionally, over- and under-representation analyses on mitotic blastomeres revealed that NUP153 association with chromatin is initiated during metaphase before the initiation of the regeneration of the lamina (P < 0.001; chi-squared goodness-of-fit test). In conclusion, rabbit embryonic development is accompanied by stage-dependent changes of the amount of nuclear invaginations carrying nuclear pores. Although cattle and mouse embryos almost exclusively feature narrow invaginations restricted to the nuclear periphery and not in contact with nucleoli, rabbit embryos feature additional wide invaginations that can reach across the nucleus and target nucleoli.

67 CORRELATION OF ARCHITECTURAL AND FUNCTIONAL REPROGRAMMING OF NUCLEI DURING EMBRYONIC GENOME ACTIVATION OF EARLY BOVINE EMBRYOS GENERATED BY IVF AND SCNT

Development of mammalian pre-implantation embryos provides an excellent model to explore interactions of nuclear organisation and nuclear functions. Based on light optical sectioning with confocal laser scanning microscopy and structured illumination microscopy, we performed a quantitative three-dimensional image analysis of nuclei in early bovine embryos generated by in vitro fertilization (IVF) and somatic cell nuclear transfer (SCNT) of bovine fibroblast nuclei. The same sequence of changes was observed in nuclei of both IVF and SCNT embryos during embryonic genome activation (EGA) is that typically achieved in embryos between 8 and 16 cells. In both pre-EGA IVF and SCNT embryos, chromosome territories (CT) were assembled as spatially distinct entities at the nuclear periphery, whereas the nuclear interior was typically occupied by a mostly chromatin free lacuna enriched with splicing factors. Detection of H3K4m3 demonstrates the presence of transcriptionally competent chromatin before EGA, which was correlated with large-scale movements of CT into the nuclear interior and a several-fold decrease of nuclear volumes. Post-EGA nuclei are characterised by a conventional nuclear architecture with chromatin distributed throughout the nuclear space, heterochromatin enriched with histone markers for transcriptionally silent chromatin beneath the nuclear lamina and around nucleoli, as well as heterochromatin clusters and chromocenters throughout the nuclear interior. Pre- and post-EGA nuclei were recorded with the superior resolution of structured illumination microscopy to allow a quantitative analysis of the nuclear topography of H3K4me3 and RNAP II signals. These signals were highly significantly enriched in the perichromatin region (PR) surrounding the compact, transcriptionally silent interior of megabase-sized chromatin domains, which form the basic structural units of CT. The PR is in direct contact with interchromatin compartment (IC) channels starting at nuclear pores, permeating the nuclear space and harboring nuclear bodies in IC lacunas. Our findings support a model for the functional nuclear architecture based on spatially distinct, but co-aligned three-dimensional networks of an active and an inactive nuclear compartment. The active nuclear compartment is built up from the structurally and functionally interacting IC and PR, whereas the inactive nuclear compartment consists of the compact, transcriptionally silent core of chromatin domain clusters. This work is supported by the DFG (ZA 425/1-3, CR 59/29-2).

106 STUDIES OF NUCLEAR ARCHITECTURE IN MAMMALIAN PRE-IMPLANTATION EMBRYOS AND EMBRYONIC STEM CELLS USING SUPER-RESOLUTION FLUORESCENCE MICROSCOPY

Three-dimensional (3-D) super-resolution fluorescence microscopy has allowed major progress in studies of the functional nuclear organization (Markaki et al. 2010 Cold Spring Harb. Symp. Quant. Biol. 75, 475–492; Markaki et al. 2012 Bioessays 34, 412–426). We have exploited these new possibilities to explore nuclear organization at different stages of bovine pre-implantation development (4-cell, 8-cell, 16-cell, morula, and blastocyst stage). In particular, we studied the topography of RNA polymerase II and the distribution of transcriptionally competent and noncompetent chromatin using antibodies against H3K4me3 and H3K27me3, respectively. For comparison, we have started analyses of mouse pre-implantation embryos and embryonic stem cells as well. Our results support the chromosome territory-interchromatin compartment (CT-IC) model (Cremer and Cremer 2010 Cold Spring Harb. Perspect. Biol. 2, a003889; Cremer et al. 2012 In: Epigenetic Regulation and Epigenomics 451–483). In all cell types, the nuclear space is occupied by chromosome territories (CTs; Koehler et al. 2009 Exp. Cell Res. 315, 2053–2063), the interchromatin compartment (IC), and one or several nucleoli. The CTs are built up from interconnected, megabase-sized chromatin domains (CDs). These ~1-Mbp CDs may consist of a series of ~100-kbp CDs (Cremer et al. 2000 Crit. Rev. Eukaryot. Gene Expr. 10, 179–212), which globally form a compact chromatin core surrounded by a layer of decondensed chromatin, called the perichromatin region. Current evidence supports the hypothesis that the perichromatin region represents the nuclear compartment, where transcription, co-transcriptional splicing, DNA-replication, and DNA-repair take place (Rouquette et al. 2010 Int. Rev. Cell Mol. Biol. 282, 1–90). The IC provides a contiguous, crowded compartment, which starts with channels at nuclear pores and pervades the chromatin compartment both between and within CTs. Small-scale chromatin loops of the perichromatin region can protrude into the interior of IC channels allowing direct contacts between CDs in cis and trans. At other sites the IC expands to wider, chromatin-free lacunas with splicing speckles and nuclear bodies. This model is in line with a fractal higher-order chromatin arrangement at all levels from CTs, chromosome arms and bands to ~1 Mbp CDs organized as fractal globules (Mirny 2011 Chromosome Res. 19, 37–51). This work is supported by the DFG (ZA 425/1-3, CR 59/29-2).

Ziele und Grenzen der Quantifizierung genetischer Risiken

In diesem Beitrag geht es um statistische Risikobewertungen im Rahmen einer genetischen Beratung und ihre Aussagekraft für persönlichen Entscheidungen Ratsuchender. Schon bei manchen Mendelschen Krankheiten und generell bei multifaktoriellen Krankheiten genügt die Angabe eines A-priori-Risikos für alle betroffenen Familien nicht. Die Frage, ob eine ratsuchende Person selbst oder ihre zukünftigen Kinder die befürchtete Krankheit mit schweren, kausal unbehandelbaren Symptomen entwickeln wird, kann sehr stark von individuellen Umständen abhängen. Dementsprechend kann es sein, dass bei einer quantitativen Erfassung solcher Umstände das daraus zu berechnende A-posteriori-Risiko für ein Individuum sehr weit nach oben oder unten abweicht. Die Quantifizierung individueller genetischer Risiken ist zurzeit aufgrund mangelnder Daten oftmals nicht möglich, sie wird aber in der genetischen Beratung der Zukunft eine immer größere Rolle spielen. Neben der Einbeziehung von Umwelteinflüssen zwingen auch die Erkenntnisse der Epigenetik zu einer Neubewertung von individuellen Risiken. So können intrauterine und frühkindliche Einflüsse langfristig wirksame epigenetische Veränderungen auslösen und physiologische Veränderungen bewirken, durch die bestimmte Krankheitsrisiken im weiteren Verlauf des Lebens signifikant beeinflusst werden. Wegen der Komplexität genetischer und epigenetischer Netzwerke ist eine Einordnung von mutierten Genen oder von krankheitsdisponierenden Allelen in „schlechte“ oder „kranke“ Gene ebenso fehl am Platz wie die Kategorisierung von Genen und Allelen mit bestimmten gesundheitsfördernden Wirkungen als „gute“ oder „gesunde“ Gene. Solche Rhetorik kann bei Menschen Schuldgefühle oder ebenso fehlgeleitete Überlegenheitsgefühle bestärken. Sie ist zudem auch politisch gefährlich, weil sie in der Öffentlichkeit einem Denken in neo-eugenischen Mustern Vorschub leistet. Im Gegensatz dazu geht es in der nichtdirektiven genetischen Beratung darum, zuverlässige Informationen für ihre persönliche Entscheidung zu vermitteln. Diese Entscheidung soll ethisch verantwortbar sein und Ratsuchenden eine realistische Perspektive eröffnen, auch langfristig mit dem in der Beratung erörterten Problem umzugehen. Schon bei Krankheiten wie Sichelzellanämie und Thalassämien zeigen die Selektionsvorteile von Heterozygoten gegenüber der Malaria tropica, warum eine genetische Bürde in einer Population nicht nur Nachteile, sondern auch Vorteile haben kann. Solche Schwierigkeiten der Bewertung dürften auch für viele Allele gelten, die seit vielen Generationen im Genpool verankert sind, obwohl sie zu multifaktoriellen Erkrankungen disponieren. In Auseinandersetzungen zur Heritabilität quantitativ verteilter, phänotypischer Merkmale wird oft der Heritabilitätskoeffizient herangezogen, um den überwiegenden Einfluss von Genen und ihren Allelen auf das fragliche Merkmal zu beweisen oder zu widerlegen. In diesem Zusammenhang erinnern die Verfasser daran, dass der Heritabilitätskoeffizient nur Aussagen zum Einfluss der in einer Population festgestellten genetischen Varianz in Relation zur Gesamtvarianz aller quantitativ fassbaren Faktoren macht, die bei dem in Frage stehenden phänotypischen Merkmal eine nachweisbare Rolle spielen. Weder macht der Heritabilitätskoeffizient eine Aussage zum absoluten Einfluss von Genen und anderen Faktoren auf das Merkmal, noch lässt sich aus diesem Koeffizienten ablesen, ob unvorhersehbare Veränderungen der Umwelt das untersuchte Merkmal und seine Heritabilität in der Zukunft stark beeinflussen könnten. Im Gegensatz zu einem weit verbreiteten Missverständnis in öffentlichen Debatten macht der Heritabilitätskoeffizient keinerlei Aussage zu den Interaktionen genetischer, epigenetischer und umweltbedingter Faktoren, die zur quantitativen Ausprägung des Merkmals bei einem Individuum beitragen. Abschließend werden die Chancen einer risikoadaptierten Prävention von Krankheiten erörtert.

Surface science and model catalysis with ionic liquid-modified materials

Materials making use of thin ionic liquid (IL) films as support-modifying functional layer open up a variety of new possibilities in heterogeneous catalysis, which range from the tailoring of gas-surface interactions to the immobilization of molecularly defined reactive sites. The present report reviews recent progress towards an understanding of "supported ionic liquid phase (SILP)" and "solid catalysts with ionic liquid layer (SCILL)" materials at the microscopic level, using a surface science and model catalysis type of approach. Thin film IL systems can be prepared not only ex-situ, but also in-situ under ultrahigh vacuum (UHV) conditions using atomically well-defined surfaces as substrates, for example by physical vapor deposition (PVD). Due to their low vapor pressure, these systems can be studied in UHV using the full spectrum of surface science techniques. We discuss general strategies and considerations of this approach and exemplify the information available from complementary methods, specifically photoelectron spectroscopy and surface vibrational spectroscopy.

Functional nuclear organization of transcription and DNA replication: a topographical marriage between chromatin domains and the interchromatin compartment

We studied the nuclear topography of RNA transcription and DNA replication in mammalian cell types with super-resolution fluorescence microscopy, which offers a resolution beyond the classical Abbe/Raleigh limit. Three-dimensional structured illumination microscopy (3D-SIM) demonstrated a network of channels and wider lacunas, called the interchromatin compartment (IC). The IC starts at nuclear pores and expands throughout the nuclear space. It is demarcated from the compact interior of higher-order chromatin domains (CDs) by a 100-200-nm thick layer of decondensed chromatin, termed the perichromatin region (PR). Nascent DNA, nascent RNA, RNA polymerase II (RNA Pol II), as well as histone modifications for transcriptionally competent/active chromatin, are highly enriched in the PR, whereas splicing speckles are observed in the interior of the IC. In line with previous electron microscopic evidence, spectral precision distance/position determination microscopy (SPDM) confirmed the presence of RNA Pol II clusters indicative of transcription factories. Still, a substantial part of transcription apparently takes place outside of such factories. Previous electron microscopic evidence has suggested that the functional nuclear organization of DNA replication depends on brownian movements of chromatin between the CD interior and the PR. As an incentive for future studies, we hypothesize that such movements also take place during transcription, i.e., only the actually transcribed part of a gene may be located within the PR, whereas its major part, including previously or later transcribed sequences, is embedded in a higher-order chromatin configuration in the interior of the CD.

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.

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.

37 REPROGRAMMING OF THE HIGHER ORDER CHROMATIN ORGANIZATION IN BOVINE NUCLEAR TRANSFER EMBRYOS

Reprogramming of nuclei after somatic cell nuclear transfer is a crucial process to reset the expression profile of the donor cell to that of a developing embryo. Reprogramming affects the epigenome of the donor nucleus, which is the complete set of epigenetic determinants that establishes and maintains a given transcriptome. These epigenetic determinants include e.g. DNA methylation, modifications of histone tails, histone variants, and other chromatin components. A less well characterized level of epigenetic gene regulation is the spatial higher order chromatin organization. In somatic cells chromosomes are organized as individual entities called chromosome territories (CTs), which localize according to their gene density with gene-rich chromosomes being in the nuclear interior, gene-poor ones at the nuclear periphery. We have shown previously that this gene density related distribution is established during major genome activation (MGA) in bovine in vitro fertilized (IVF) embryos, while embryos up to the 8-cell stage do not show a difference in their CT localization. In the present study, we investigated whether the gene density related distribution of chromosomes present in bovine fibroblasts is reprogrammed after nuclear transfer (NT), i.e. erased to restore the situation found in IVF embryos. Moreover, we analyzed if a gene density related CT arrangement is re-established at the same time point as in IVF embryos, i.e. during MGA. Therefore we analyzed the nuclear distribution of bovine chromosome 19 (19 genes Mb–1) and 20 (5 genes Mb–1) in one-, 2- and 4-cell NT embryos as pre-MGA stages and in embryos with 10–20 nuclei cells–1, representing embryos during MGA. CTs were visualized via a recently developed protocol utilizing fluorescence in situ hybridization (FISH) on three dimensionally preserved embryos. In 1- and 2-cell embryos we could not detect a gene density related CT distribution arguing for a rapid reprogramming, i.e. erasure of the positional information previously present in the donor nuclei. Surprisingly, we observed a precocious establishment of a gene density related distribution already at the 4-cell stage that became more pronounced in 10–20-cell embryos, when this specific CT distribution is established in IVF embryos. We conclude that the spatial arrangement of chromosomes is an epigenetic parameter that is rapidly reprogrammed upon nuclear transfer of a somatic nucleus, exposed to the oocyte cytoplasm. Moreover, the gene density related positioning of chromosomes in bovine NT embryos is re-established earlier than in IVF embryos, suggesting a possible involvement in early developmental failures of NT embryos. Funded by the Deutsche Forschungsgemeinschaft (ZA 425/1-2, CR 59/26-1).

Spatial quantitative analysis of fluorescently labeled nuclear structures: problems, methods, pitfalls

The vast majority of microscopic data in biology of the cell nucleus is currently collected using fluorescence microscopy, and most of these data are subsequently subjected to quantitative analysis. The analysis process unites a number of steps, from image acquisition to statistics, and at each of these steps decisions must be made that may crucially affect the conclusions of the whole study. This often presents a really serious problem because the researcher is typically a biologist, while the decisions to be taken require expertise in the fields of physics, computer image analysis, and statistics. The researcher has to choose between multiple options for data collection, numerous programs for preprocessing and processing of images, and a number of statistical approaches. Written for biologists, this article discusses some of the typical problems and errors that should be avoided. The article was prepared by a team uniting expertise in biology, microscopy, image analysis, and statistics. It considers the options a researcher has at the stages of data acquisition (choice of the microscope and acquisition settings), preprocessing (filtering, intensity normalization, deconvolution), image processing (radial distribution, clustering, co-localization, shape and orientation of objects), and statistical analysis.

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.

107 CHANGES OF HIGHER ORDER CHROMATIN ARRANGEMENTS CORRELATE WITH GENOME ACTIVATION DURING EARLY BOVINE DEVELOPMENT

In interphase nuclei of higher eukaryotes, the genome is organized within discrete chromosome territories (CT). These CT are arranged in a nonrandom fashion depending on cell type, species, and cell cycle stage. Gene-rich CT locate more internally in the nucleus, whereas gene-poor ones are found more peripherally. So far, CT have been investigated mainly in cultured cells and to some extent in tissues, yet little is known about the origin and fate of CT during early development. To gain insights into the very early organization of CT in embryos, we developed a fluorescence in situ hybridization protocol that yields optimal results with 3 dimensionally preserved bovine embryos. Using this protocol, we investigated CT of bovine chromosome 19 and 20. These chromosomes represent the gene-richest and gene-poorest chromosomes, according to the number of annotated genes at the Ensembl database (www.ensembl.org). We could confirm a gene density-related radial nuclear distribution in bovine fibroblasts and lymphocytes with CT 19 being more interior than CT 20. Because cell cycle-dependent effects were not expected in view of published data in other species, we did not consider the cell cycle stage of the investigated specimen. In early bovine embryos generated by in vitro fertilization, we demonstrated the existence of nonoverlapping CT already in zygotic pronuclei. In day 3 embryos, but interestingly not in day 2 embryos, a gene density-related radial distribution of CT 19 and 20 was observed. Because these stages represent a transition stage during which the embryonic genome is activated, our results indicate a correlation between genome activation and changes of higher order nuclear organization. We are currently investigating the question whether transcription is a prerequisite for the establishment of a gene density-related chromosome positioning, as well as how reprogramming after nuclear transfer affects CT distribution of somatic donor nuclei. The present work is supported by the Deutsche Forschungsgemeinschaft (ZA 425/1).

141 INDICATIONS FOR DNA DOUBLE-STRAND BREAK REPAIR IN EARLY BOVINE EMBRYOS

DNA double-strand breaks (DSBs) are considered the most severe type of DNA lesions, because such lesions, if unrepaired, lead to a loss of genome integrity. Soon after induction of DSBs, chromatin surrounding the damage is modified by phosphorylation of the histone variant H2AX, generating so-called γH2AX, which is a hallmark of DSBs (Takahashi et al. 2005 Cancer Lett. 229, 171–179). γH2AX appears to be a signal for the recruitment of proteins constituting the DNA repair machinery. Depending on the type of damage and the cell cycle stage of the affected cell, DSBs are repaired either by nonhomologous end joining or by homologous recombination using the sister chromatid DNA as template (Hoeijmakers 2001 Nature 411, 366–374). We used immunofluorescence to analyze chromatin composition during bovine development and found γH2AX foci in both male and female pronuclei of IVF embryos. The number and size of foci varied considerably between embryos and between the male and female pronuclei. To test whether the observed γH2AX foci represented sites of active DNA repair, we co-stained IVF zygotes for γH2AX and 3 different proteins involved in homologous recombination repair of DSBs: NBS1 (phosphorylated at amino acid serine 343), 53BP1, and Rad51. We found co-localization of γH2AX foci with phosphorylated NBS1 as well as with Rad51 but did not observe the presence of 53BP1 at γH2AX foci in IVF zygotes. Our finding shows the presence of DSBs in IVF zygotes and suggests the capability of homologous recombination repair. The lack of 53BP1, a component of homologous recombination repair, which usually co-localizes with γH2AX foci at exogenously induced DSBs (Schultz et al. 2000 J. Cell. Biol. 151, 1381–1390) poses the possibility that the mechanism present in early embryos differs substantially from that involved in DNA repair of DSBs in somatic cells.

Rise, fall and resurrection of chromosome territories: a historical perspective. Part II. Fall and resurrection of chromosome territories during the 1950s to 1980s. Part III. Chromosome territories and the functional nuclear architecture: experiments and models from the 1990s to the present

Part II of this historical review on the progress of nuclear architecture studies points out why the original hypothesis of chromosome territories from Carl Rabl and Theodor Boveri (described in part I) was abandoned during the 1950s and finally proven by compelling evidence forwarded by laser-uv-microbeam studies and in situ hybridization experiments. Part II also includes a section on the development of advanced light microscopic techniques breaking the classical Abbe limit written for readers with little knowledge about the present state of the theory of light microscopic resolution. These developments have made it possible to perform 3D distance measurements between genes or other specifically stained, nuclear structures with high precision at the nanometer scale. Moreover, it has become possible to record full images from fluorescent structures and perform quantitative measurements of their shapes and volumes at a level of resolution that until recently could only be achieved by electron microscopy. In part III we review the development of experiments and models of nuclear architecture since the 1990s. Emphasis is laid on the still strongly conflicting views about the basic principles of higher order chromatin organization. A concluding section explains what needs to be done to resolve these conflicts and to come closer to the final goal of all studies of the nuclear architecture, namely to understand the implications of nuclear architecture for nuclear functions.

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.

DNA-repair protein distribution along the tracks of energetic ions

A simple model of homogenous chromatin distribution in HeLa-cell nuclei suggests that the track of an energetic ion hits 30 nm chromatin fibers with a mean distance of 0.55 mum. To test this assumption, living HeLa-cells were irradiated at the irradiation setup of the ion microprobe SNAKE using the ion beams provided by the Munich 14 MV tandem accelerator. After irradiation, the distribution of 53BP1 protein foci was studied by immunofluorescence. The observed 53BP1 distribution along the tracks of 29 MeV (7)Li ions and 24 MeV (12)C ions differed significantly from the expectations resulting from the simple chromatin model, suggesting that the biological track structure is determined by cell nuclear architecture with higher order organisation of chromatin.

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 Δ5) 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 Δ5 can bind to the c-myc promoter with the same efficiency as wild type Pol II. However, Pol II Δ5 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 Δ5 or wildtype Pol II revealed a single, highly mobile Pol II Δ5 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.

Microirradiation of cells with energetic heavy ions

The ion microprobe SNAKE at the Munich 14 MV tandem accelerator achieves beam focussing by a superconducting quadrupole doublet and can make use of a broad range of ions and ion energies, from 20 MeV protons to 200 MeV gold ions. Because of these properties, SNAKE is particularly attractive for biological microbeam experiments. Here we describe the adaptation of SNAKE for microirradiation of cell samples. This includes enlarging of the focal distance in order to adjust the focal plane to the specimen stage of a microscope, construction of a beam exit window in a flexible nozzle and of a suitable cell containment, as well as development of procedures for on-line focussing of the beam, preparation of single ions and scanning by electrostatic deflection of the beam. When irradiating with single 100 MeV (16)O ions, the adapted set-up permits an irradiation accuracy of 0.91 microm (full width at half maximum) in the x-direction and 1.60 microm in the y-direction, as demonstrated by retrospective track etching of polycarbonate foils. Accumulation of the repair protein Rad51, as detected by immunofluorescence, was used as a biological track detector after irradiation of HeLa cells with geometric patterns of counted ions. Observed patterns of fluorescence foci agreed reasonably well with irradiation patterns, indicating successful adaptation of SNAKE. In spite of single ion irradiation, we frequently observed split fluorescence foci which might be explained by small-scale chromatin movements.

Three dimensional analysis of histone methylation patterns in normal and tumor cell nuclei

Histone modifications represent an important epigenetic mechanism for the organization of higher order chromatin structure and gene regulation. Methylation of position-specific lysine residues in the histone H3 and H4 amino termini has linked with the formation of constitutive and facultative heterochromatin as well as with specifically repressed single gene loci. Using an antibody, directed against dimethylated lysine 9 of histone H3 and several other lysine methylation sites, we visualized the nuclear distribution pattern of chromatin flagged by these methylated lysines in 3D preserved nuclei of normal and malignant cell types. Optical confocal serial sections were used for a quantitative evaluation. We demonstrate distinct differences of these histone methylation patterns among nuclei of different cell types after exit of the cell cycle. Changes in the pattern formation were also observed during the cell cycle. Our data suggest an important role of methylated histones in the reestablishment of higher order chromatin arrangements during telophase/early G1. Cell type specific histone methylation patterns are possibly casually involved in the formation of cell type specific heterochromatin compartments, composed of (peri)centromeric regions and chromosomal subregions from neighboring chromosomes territories, which contain silent genes.

A new system for laser-UVA-microirradiation of living cells

Local nuclear irradiation of living cells has been used to gain insight into the dynamic changes that cell nuclei undergo in response to DNA damage. In particular, the effects of DNA double-strand breaks (DSBs), a major threat to the genomic integrity of cells, have been studied by local nuclear irradiation with ionizing radiation. This method has the disadvantage that it requires expensive equipment to generate a sufficiently high density of focused or collimated ionizing radiation. After appropriate sensitization of the cellular DNA, nuclear microirradiation with UVA can also produce DSBs. In this communication we present a semi-automatic system for laser-UVA-microirradiation based on a commercial laser scanning microscope. The system allows the convenient selection and precise irradiation of living cells, and could provide the basis for a more widespread availability of microirradiation facilities for DNA-repair research.

Non-random radial higher-order chromatin arrangements in nuclei of diploid human cells

A quantitative comparison of higher-order chromatin arrangements was performed in human cell types with three-dimensionally (3D) preserved, differently shaped nuclei. These cell types included flat-ellipsoid nuclei of diploid amniotic fluid cells and fibroblasts and spherical nuclei of B and T lymphocytes from peripheral human blood. Fluorescence in-situ hybridization (FISH) was performed with chromosome paint probes for large (#1-5) and small (#17-20) autosomes, and for the two sex chromosomes. Other probes delineated heterochromatin blocks of numerous larger and smaller human chromosomes. Shape differences correlated with distinct differences in higher order chromatin arrangements: in the spherically shaped lymphocyte nuclei we noted the preferential positioning of the small, gene dense #17, 19 and 20 chromosome territories (CTs) in the 3D nuclear interior--typically without any apparent connection to the nuclear envelope. In contrast, CTs of the gene-poor small chromosomes #18 and Y were apparently attached at the nuclear envelope. CTs of large chromosomes were also preferentially located towards the nuclear periphery. In the ellipsoid nuclei of amniotic fluid cells and fibroblasts, all tested CTs showed attachments to the upper and/or lower part of the nuclear envelope: CTs of small chromosomes, including #18 and Y, were located towards the centre of the nuclear projection (CNP), while the large chromosomes were positioned towards the 2D nuclear rim. In contrast to these highly reproducible radial arrangements, 2D distances measured between heterochromatin blocks of homologous and heterologous CTs were strikingly variable. These results as well as CT painting let us conclude that nuclear functions in the studied cell types may not require reproducible side-by-side arrangements of specific homologous or non-homologous CTs. 3D-modelling of statistical arrangements of 46 human CTs in spherical nuclei was performed under the assumption of a linear correlation between DNA content of each chromosome and its CT volume. In a set of modelled nuclei, we noted the preferential localization of smaller CTs towards the 3D periphery and of larger CTs towards the 3D centre. This distribution is in clear contrast to the experimentally observed distribution in lymphocyte nuclei. We conclude that presently unknown factors (other than topological constraints) may play a decisive role to enforce the different radial arrangements of large and small CTs observed in ellipsoid and spherical human cell nuclei.

Arrangements of macro- and microchromosomes in chicken cells

Arrangements of chromosome territories in nuclei of chicken fibroblasts and neurons were analysed employing multicolour chromosome painting, laser confocal scanning microscopy and three-dimensional (3D) reconstruction. The chicken karyotype consists of 9 pairs of macrochromosomes and 30 pairs of microchromosomes. Although the latter represent only 23% of the chicken genome they containalmost 50% of its genes. We show that territories of microchromosomes in fibroblasts and neurons were clustered within the centre of the nucleus, while territories of the macrochromosomes were preferentially located towards the nuclear periphery. In contrast to these highly consistent radial arrangements, the relative arrangements of macrochromosome territories with respect to each other (side-by-side arrangements) were variable. A stringent radial arrangement of macro- and microchromosomes was found in mitotic cells. Replication labelling studies revealed a pattern of DNA replication similar to mammalian cell nuclei: gene dense, early replicating chromatin mostly represented by microchromosomes, was located within the nuclear interior, surrounded by a rim of late replicating chromatin. These results support the evolutionary conservation of several features of higher-order chromatin organization between mammals and birds despite the differences in their karyotypes.

Morphology and dynamics of chromosome territories in living cells

Chromosome territories formed by fluorescence-labeled sub-chromosomal foci were analyzed in time-lapse series of 3D confocal data sets of living HeLa and human neuroblastoma cells. The quantitative analysis of the chromosome territory morphology confirmed previous results obtained by visual observation [Zink et al., Hum. Genet. 102 (1998) 241-251] that chromosome territories persisted as stable entities over an observation time >4 h. The changes in morphology with time of single chromosome territories were found to be less pronounced than differences in morphology of different chromosome territories in fixed cells. The analysis of the individual motion of chromosome territories recently showed 'Brownian' diffusion-like motion at very slow rates [Bornfleth et al., Biophys. J. 77 (1999) 2871-2886]. Here, we show that the mutual motion of different chromosome territories was independent and also 'Brownian' diffusion-like.

Remodeling of donor nuclei, DNA-synthesis, and ploidy of bovine cumulus cell nuclear transfer embryos: effect of activation protocol

The purpose of this study was to investigate the effects of two activation protocols on nuclear remodeling, DNA synthesis during the first cell cycle, chromosome segregation after first mitosis and development to blastocyst of embryos produced by somatic nuclear transfer. Pronuclear formation was significantly higher when activation lasted 5 hr compared to 3 hr for both ethanol-cycloheximide and ionomycin-bohemine treatment. However, the presence of a single nucleus was significantly higher in embryos activated for 3 hr in bohemine. Initiation of DNA synthesis was delayed in ethanol-cycloheximide group, however, after 12 hr labeling 100% of embryos synthesized DNA in both groups. Embryos activated with ethanol-cycloheximide developed to blastocysts at a significantly higher rate than those activated with ionomycin-bohemine. Analysis of 2-cell embryos with DNA probes for chromosome 6, 7, and 15 by fluorescence in situ hybridization showed that at least 50% of NT embryos were of normal ploidy independent of the activation stimulus. The results presented in this study show differences between the protocols compared on the nuclear events during the first cell cycle and on the development to blastocyst. Mol. Reprod. Dev. 59: 371-379, 2001.

Chromosome territories, nuclear architecture and gene regulation in mammalian cells

The expression of genes is regulated at many levels. Perhaps the area in which least is known is how nuclear organization influences gene expression. Studies of higher-order chromatin arrangements and their dynamic interactions with other nuclear components have been boosted by recent technical advances. The emerging view is that chromosomes are compartmentalized into discrete territories. The location of a gene within a chromosome territory seems to influence its access to the machinery responsible for specific nuclear functions, such as transcription and splicing. This view is consistent with a topological model for gene regulation.

Chromosome territories, interchromatin domain compartment, and nuclear matrix: an integrated view of the functional nuclear architecture

Advances in the specific fluorescent labeling of chromatin in fixed and living human cells in combination with three-dimensional (3D) and 4D (space plus time) fluorescence microscopy and image analysis have opened the way for detailed studies of the dynamic, higher-order architecture of chromatin in the human cell nucleus and its potential role in gene regulation. Several features of this architecture are now well established: 1. Chromosomes occupy distinct territories in the cell nucleus with preferred nuclear locations, although there is no evidence of a rigid suprachromosomal order. 2. Chromosome territories (CTs) in turn contain distinct chromosome arm domains and smaller chromatin foci or domains with diameters of some 300 to 800 nm and a DNA content in the order of 1 Mbp. 3. Gene-dense, early-replicating and gene-poor, middle-to-late-replicating chromatin domains exhibit different higher-order nuclear patterns that persist through all stages of interphase. In mitotic chromosomes early replicating chromatin domains give rise to Giemsa light bands, whereas middle-to-late-replicating domains form Giemsa dark bands and C-bands. In an attempt to integrate these experimental data into a unified view of the functional nuclear architecture, we present a model of a modular and dynamic chromosome territory (CT) organization. We propose that basically three nuclear compartments exist, an "open" higher-order chromatin compartment with chromatin domains containing active genes, a "closed" chromatin compartment comprising inactive genes, and an interchromatin domain (ICD) compartment (Cremer et al., 1993; Zirbel et al., 1993) that contains macromolecular complexes for transcription, splicing, DNA replication, and repair. Genes in "open," but not in "closed" higher-order chromatin compartments have access to transcription and splicing complexes located in the ICD compartment. Chromatin domains that build the "open" chromatin compartment are organized in a way that allows the direct contact of genes and nascent RNA to transcription and splicing complexes, respectively, preformed in the ICD compartment. In contrast, chromatin domains that belong to the "closed" compartment are topologically arranged and compacted in a way that precludes the accessibility of genes to transcription complexes. We argue that the content of the ICD compartment is highly enriched in DNA depleted biochemical matrix preparations. The ICD compartment may be considered as the structural and functional equivalent of the in vivo nuclear matrix. A matrix in this functional sense is compatible with but does not necessitate the concept of a 3D nuclear skeleton existing of long, extensively arborized filaments. In the absence of unequivocal evidence for such a structural matrix in the nucleus of living cells we keep an agnostic attitude about its existence and possible properties in maintaining the higher-order nuclear architecture. Quantitative modeling of the 3D and 4D human genome architecture in situ shows that such an assumption is not necessary to explain presently known aspects of the higher-order nuclear architecture. We expect that the interplay of quantitative modeling and experimental tests will result in a better understanding of the compartmentalized nuclear architecture and its functional consequences.

Topology of double minutes (dmins) and homogeneously staining regions (HSRs) in nuclei of human neuroblastoma cell lines

Amplification of the MYCN gene is a characteristic feature of many neuroblastomas and is correlated with aggressive tumor growth. Amplicons containing this gene form either double minutes (dmins) or homogeneously staining regions (HSRs). To study the nuclear topology of these tumor-specific and transcriptionally active chromatin structures in comparison to chromosome territories, we performed fluorescence in situ hybridization with a MYCN probe and various chromosome paint probes, confocal laser scanning microscopy, and quantitative three-dimensional image analysis. The dmins formed dot-like structures in interphase nuclei and were typically located at the periphery of complexly folded chromosome territories; dmins noted in the chromosome territory interior were often detected within an invagination of the territory surface. Interphase HSRs typically formed extremely expanded structures, which we have never observed for chromosome territories of normal and tumor cell nuclei. Stretches of HSR-chromatin often extended throughout a large part of the cell nucleus, but appeared well separated from neighboring chromosome territories. We hypothesize that dmins are located within the interchromosomal domain (ICD) space and that stretches of HSR-chromatin align along this space. Such a topology could facilitate access of amplified genes to transcription and splicing complexes that are assumed to localize in the ICD space.

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.

Molecular evidence for derivation of metastatic cells from minor subclones of primary clear renal cell carcinomas

The production of metastases depends on changes in a large number of genes. It is also connected with the interaction of tumor cells with the environment. It has been reported that primary tumor clone domination is also an important factor in metastasizing, and in many neoplasms dominating clones are the metastatic forerunners. Up to now it is unknown whether domination of a given clone in a primary renal cell carcinoma is a crucial factor in forming metastases or rather presence or absence of specific genes imposes the major advantage in the metastatic process. To study the presence or absence of the duplication and mitotic nondisjunction event as one of the phenomenon in the creation of metastases, as well as possible derivation of metastatic cells from the minor subclone of primary tumor, we examined three metastatic renal clear-cell carcinomas in which by comparative genomic hybridization we detected the loss of 3p in the primary tumor and two copies of 3p in the corresponding metastasis. Loss of heterozygosity analyses using markers for 3p25 (D3S1038), 3p21.1 (D3S1295), and 3p14.2 (D3S1481) proved heterozygosity of at least two 3p loci in all metastatic tumors, which indicates the absence of mitotic nondisjunction event as a cause of occurrence of two copies of 3p in metastases. Our results suggest that in some of the clear-cell renal carcinomas metastatic cells may derive from minor subclones of primary tumors.