Anaphase chromatid motion: involvement of type II DNA topoisomerases

Simulation of Different Three-Dimensional Models of Whole Interphase Nuclei Compared to Experiments - A Consistent Scale-Bridging Simulation Framework for Genome Organization

The three-dimensional architecture of chromosomes, their arrangement, and dynamics within cell nuclei are still subject of debate. Obviously, the function of genomes-the storage, replication, and transcription of genetic information-has closely coevolved with this architecture and its dynamics, and hence are closely connected. In this work a scale-bridging framework investigates how of the 30 nm chromatin fibre organizes into chromosomes including their arrangement and morphology in the simulation of whole nuclei. Therefore, mainly two different topologies were simulated with corresponding parameter variations and comparing them to experiments: The Multi-Loop-Subcompartment (MLS) model, in which (stable) small loops form (stable) rosettes, connected by chromatin linkers, and the Random-Walk/Giant-Loop (RW/GL) model, in which large loops are attached to a flexible non-protein backbone, were simulated for various loop and linker sizes. The 30 nm chromatin fibre was modelled as a polymer chain with stretching, bending and excluded volume interactions. A spherical boundary potential simulated the confinement to nuclei with different radii. Simulated annealing and Brownian Dynamics methods were applied in a four-step decondensation procedure to generate from metaphase decondensated interphase configurations at thermodynamical equilibrium. Both the MLS and the RW/GL models form chromosome territories, with different morphologies: The MLS rosettes result in distinct subchromosomal domains visible in electron and confocal laser scanning microscopic images. In contrast, the big RW/GL loops lead to a mostly homogeneous chromatin distribution. Even small changes of the model parameters induced significant rearrangements of the chromatin morphology. The low overlap of chromosomes, arms, and subchromosomal domains observed in experiments agrees only with the MLS model. The chromatin density distribution in CLSM image stacks reveals a bimodal behaviour in agreement with recent experiments. Combination of these results with a variety of (spatial distance) measurements favour an MLS like model with loops and linkers of 63 to 126 kbp. The predicted large spaces between the chromatin fibres allow typically sized biological molecules to reach nearly every location in the nucleus by moderately obstructed diffusion and is in disagreement with the much simplified assumption that defined channels between territories for molecular transport as in the Interchromosomal Domain (ICD) hypothesis exist and are necessary for transport. All this is also in agreement with recent selective high-resolution chromosome interaction capture (T2C) experiments, the scaling behaviour of the DNA sequence, the dynamics of the chromatin fibre, the diffusion of molecules, and other measurements. Also all other chromosome topologies can in principle be excluded. In summary, polymer simulations of whole nuclei compared to experimental data not only clearly favour only a stable loop aggregate/rosette like genome architecture whose local topology is tightly connected to the global morphology and dynamics of the cell nucleus and hence can be used for understanding genome organization also in respect to diagnosis and treatment. This is in agreement with and also leads to a general novel framework of genome emergence, function, and evolution.

Synergy of topoisomerase and structural-maintenance-of-chromosomes proteins creates a universal pathway to simplify genome topology

Topological entanglements severely interfere with important biological processes. For this reason, genomes must be kept unknotted and unlinked during most of a cell cycle. Type II topoisomerase (TopoII) enzymes play an important role in this process but the precise mechanisms yielding systematic disentanglement of DNA in vivo are not clear. Here we report computational evidence that structural-maintenance-of-chromosomes (SMC) proteins-such as cohesins and condensins-can cooperate with TopoII to establish a synergistic mechanism to resolve topological entanglements. SMC-driven loop extrusion (or diffusion) induces the spatial localization of essential crossings, in turn catalyzing the simplification of knots and links by TopoII enzymes even in crowded and confined conditions. The mechanism we uncover is universal in that it does not qualitatively depend on the specific substrate, whether DNA or chromatin, or on SMC processivity; we thus argue that this synergy may be at work across organisms and throughout the cell cycle.

Simulation of different three-dimensional polymer models of interphase chromosomes compared to experiments-an evaluation and review framework of the 3D genome organization

Despite all the efforts the three-dimensional higher-order architecture and dynamics in the cell nucleus are still debated. The regulation of genes, their transcription, replication, as well as differentiation in Eukarya is, however, closely connected to this architecture and dynamics. Here, an evaluation and review framework is setup to investigate the folding of a 30 nm chromatin fibre into chromosome territories by comparing computer simulations of two different chromatin topologies to experiments: The Multi-Loop-Subcompartment (MLS) model, in which small loops form rosettes connected by chromatin linkers, and the Random-Walk/Giant-Loop (RW/GL) model, in which large loops are attached to a flexible non-protein backbone, were simulated for various loop, rosette, and linker sizes. The 30 nm chromatin fibre was modelled as a polymer chain with stretching, bending, and excluded volume interactions. A spherical boundary potential simulated the confinement by other chromosomes and the nuclear envelope. Monte Carlo and Brownian Dynamics methods were applied to generate chain configurations at thermodynamic equilibrium. Both the MLS and the RW/GL models form chromosome territories, with different morphologies: The MLS rosettes form distinct subchromosomal domains, compatible in size as those from light microscopic observations. In contrast, the big RW/GL loops lead to a more homogeneous chromatin distribution. Only the MLS model agrees with the low overlap of chromosomes, their arms, and subchromosomal domains found experimentally. A review of experimental spatial distance measurements between genomic markers labelled by FISH as a function of their genomic separation from different publications and comparison to simulated spatial distances also favours an MLS-like model with loops and linkers of 63 to 126 kbp. The chromatin folding topology also reduces the apparent persistence length of the chromatin fibre to a value significantly lower than the free solution persistence length, explaining the low persistence lengths found various experiments. The predicted large spaces between the chromatin fibres allow typically sized biological molecules to reach nearly every location in the nucleus by moderately obstructed diffusion and disagrees with the much simplified assumption that defined channels between territories for molecular transport as in the Interchromosomal Domain (ICD) hypothesis exist. All this is also in agreement with recent selective high-resolution chromosome interaction capture (T2C) experiments, the scaling behaviour of the DNA sequence, the dynamics of the chromatin fibre, the nuclear diffusion of molecules, as well as other experiments. In summary, this polymer simulation framework compared to experimental data clearly favours only a quasi-chromatin fibre forming a stable multi-loop aggregate/rosette like genome organization and dynamics whose local topology is tightly connected to the global morphology and dynamics of the cell nucleus.

Control of the flow properties of DNA by topoisomerase II and its targeting inhibitor

The flow properties of DNA are important for understanding cell division and, indirectly, cancer therapy. DNA topology controlling enzymes such as topoisomerase II are thought to play an essential role. We report experiments showing how double-strand passage facilitated by topoisomerase II controls DNA rheology. For this purpose, we have measured the elastic storage and viscous loss moduli of a model system comprising bacteriophage λ-DNA and human topoisomerase IIα using video tracking of the Brownian motion of colloidal probe particles. We found that the rheology is critically dependent on the formation of temporal entanglements among the DNA molecules with a relaxation time of ∼1 s. We observed that topoisomerase II effectively removes these entanglements and transforms the solution from an elastic physical gel to a viscous fluid depending on the consumption of ATP. A second aspect of this study is the effect of the generic topoisomerase II inhibitor adenylyl-imidodiphosphate (AMP-PNP). In mixtures of AMP-PNP and ATP, the double-strand passage reaction gets blocked and progressively fewer entanglements are relaxed. A total replacement of ATP by AMP-PNP results in a temporal increase in elasticity at higher frequencies, but no transition to an elastic gel with fixed cross-links.

Numerical simulation of gel electrophoresis of DNA knots in weak and strong electric fields

Gel electrophoresis allows one to separate knotted DNA (nicked circular) of equal length according to the knot type. At low electric fields, complex knots, being more compact, drift faster than simpler knots. Recent experiments have shown that the drift velocity dependence on the knot type is inverted when changing from low to high electric fields. We present a computer simulation on a lattice of a closed, knotted, charged DNA chain drifting in an external electric field in a topologically restricted medium. Using a Monte Carlo algorithm, the dependence of the electrophoretic migration of the DNA molecules on the knot type and on the electric field intensity is investigated. The results are in qualitative and quantitative agreement with electrophoretic experiments done under conditions of low and high electric fields.

The dynamics of homologous chromosome pairing during male Drosophila meiosis

BACKGROUND

Meiotic pairing is essential for the proper orientation of chromosomes at the metaphase plate and their subsequent disjunction during anaphase I. In male Drosophila melanogaster, meiosis occurs in the absence of recombination or a recognizable synaptonemal complex (SC). Due to limitations in available cytological techniques, the early stages of homologous chromosome pairing in male Drosophila have not been observed, and the mechanisms involved are poorly understood.

RESULTS

Chromosome tagging with GFP-Lac repressor protein allowed us to track, for the first time, the behavior of meiotic chromosomes at high resolution, live, at all stages of male Drosophila meiosis. Homologous chromosomes pair throughout the euchromatic regions in spermatogonia and during the early phases of spermatocyte development. Extensive separation of homologs and sister chromatids along the chromosome arms occurs in mid-G2, several hours before the first meiotic division, and before the G2/M transition. Centromeres, on the other hand, show complex association patterns, with specific homolog pairing taking place in mid-G2. These changes in chromosome pairing parallel changes in large-scale chromosome organization.

CONCLUSIONS

Our results suggest that widespread interactions along the euchromatin are required for the initiation, but not the maintenance, of meiotic pairing of autosomes in male Drosophila. We propose that heterochromatic associations, or chromatid entanglement, may be responsible for the maintenance of homolog association during late G2. Our data also suggest that the formation of chromosome territories in the spermatocyte nucleus may play an active role in ensuring the specificity of meiotic pairing in late prophase by disrupting interactions between nonhomologous chromosomes.

Topoisomerase II can unlink replicating DNA by precatenane removal

We have analysed the role of topoisomerase II (topo II) in plasmid DNA replication in Xenopus egg extracts, using specific inhibitors and two-dimensional gel electrophoresis of replication products. Topo II is dispensable for nuclear assembly and complete replication of plasmid DNA but is required for plasmid unlinking. Extensive unlinking can occur in the absence of mitosis. Replication intermediates generated in the absence of topo II activity have an increased positive superhelical stress (+DeltaLk), suggesting a deficiency in precatenane removal. The geometry of replication intermediates cut by poisoning topo II with etoposide and purified by virtue of their covalent attachment to topo II subunits demonstrates that topo II acts behind the forks at all stages of elongation. These results provide direct evidence for unlinking replicating DNA by precatenane removal and reveal a division of labour between topo I and topo II in this eukaryotic system. We discuss the role of chromatin structure in driving DNA unlinking during S phase.

DNA crossovers and type II DNA topoisomerases: A thermodynamical study

We present a theoretical study of the interaction of tight DNA crossovers with eukaryotic type II DNA topoisomerases. A quantitative analysis of the role of the enzyme during anaphase first shows that a tight DNA crossover should be an intermediate of the strand-passage reaction. We then focus on the initial steps of the strand-passage reaction in vitro which lead to the formation of a ternary complex ES1S2 between the enzyme and a tight DNA crossover (where E is the enzyme, S1 (respectively S2) is the first (respectively the second) DNA segment bound by the enzyme, and S1S2 is a tight crossover). This formation can be described by three equilibrium association constants: KS1 (for the reaction E+S1left arrow over right arrow ES1), KS2 (for ES1+S2left arrow over right arrow ES1S2), and KS (for E+S1S2left arrow over right arrow ES1S2) Using published experimental data obtained on the Drosophila enzyme, we derive rough estimates for the intrinsic equilibrium constants KS1 ( approximately 2.5x10(6) M-1) and KS2 ( approximately 10(4) M-1) and for Ks. The huge value found for Ks, about 5x10(16) M-1, suggests that the ternary complex bears a close resemblance with a transition state complex, and is consistent with the notion of a capture of the crossover by a protein clamp. We give a theoretical description of analogues of tight DNA crossovers which consist of two DNA segments stabilized by a covalent crosslinking. Such analogues are predicted to bind the enzyme with a high affinity and should be useful tools for the study of the enzyme.

A polymer model for the structural organization of chromatin loops and minibands in interphase chromosomes

A quantitative model of interphase chromosome higher-order structure is presented based on the isochore model of the genome and results obtained in the field of copolymer research. G1 chromosomes are approximated in the model as multiblock copolymers of the 30-nm chromatin fiber, which alternately contain two types of 0.5- to 1-Mbp blocks (R and G minibands) differing in GC content and DNA-bound proteins. A G1 chromosome forms a single-chain string of loop clusters (micelles), with each loop approximately 1-2 Mbp in size. The number of approximately 20 loops per micelle was estimated from the dependence of geometrical versus genomic distances between two points on a G1 chromosome. The greater degree of chromatin extension in R versus G minibands and a difference in the replication time for these minibands (early S phase for R versus late S phase for G) are explained in this model as a result of the location of R minibands at micelle cores and G minibands at loop apices. The estimated number of micelles per nucleus is close to the observed number of replication clusters at the onset of S phase. A relationship between chromosomal and nuclear sizes for several types of higher eukaryotic cells (insects, plants, and mammals) is well described through the micelle structure of interphase chromosomes. For yeast cells, this relationship is described by a linear coil configuration of chromosomes.

Quantitative immunofluorescence and immunoelectron microscopy of the topoisomerase II alpha associated with nuclear matrices from wild-type and drug-resistant chinese hamster ovary cell lines

Topo II alpha is considered an important constituent of the nuclear matrix, serving as a fastener of DNA loops to the underlying filamentous scaffolding network. To further define a mechanism of drug resistance to topo II poisons, we studied the quantity of topo II alpha associated with the nuclear matrix in drug-resistant SMR16 and parental cells in the presence and absence of VP-16. Nuclear matrices were prepared from nuclei isolated in EDTA buffer, followed by nuclease digestion with DNase II in the absence of RNase treatment and extraction with 2 M NaCl. Whole-mount spreading of residual structures permits, by means of isoform-specific antibody and colloidal-gold secondary antibodies, an estimate of the amount of topo II alpha in individual nuclear matrices. There are significant variations in topo II alpha amounts between individual nuclear matrices due to the cell cycle distribution. The parental cell line contained eight to ten times more nuclear matrix-associated topo II alpha than the resistant cell line matrices. Nuclear matrix-associated topo II alpha from wild-type and resistant cell lines correlated well with the immunofluorescent staining of the enzyme in nuclei of intact cells. The amount of DNA associated with residual nuclear structures was five times greater in the resistant cell line. This quantity of DNA was not proportional to the quantity of topo II alpha in the same matrix; in fact they were inversely related. In situ whole-mount nuclear matrix preparations were obtained from cells grown on grids and confirmed the results from labeling of isolated residual structures.

Forces on chromosomal DNA during anaphase

In the course of anaphase, the chromosomal DNA is submitted to the traction of the spindle. Several physical problems are associated with this action. In particular, the sister chromatids are generally topologically intertwined at the onset of anaphase, and the removal of the intertwinings results from a coupling between the enzymatic action of type II DNA topoisomerases and the force exerted by the spindle. We propose a physical analysis of some of these problems: 1) We compare the maximum force the spindle can produce with the force required to break a DNA molecule, and define the conditions compatible with biological safety during anaphase. 2) We show that the behavior of the sister chromatids in the absence of type II DNA topoisomerases can be described by two distinct models: a chain pullout model accounts for the experimental observations made in the budding yeast, and a model of the mechanical rupture of rubbers accounts for the nondisjunction in standard cases. 3) Using the fluctuation-dissipation theorem, we introduce an effective protein friction associated with the strand-passing activity of type II DNA topoisomerases. We show that this friction can be used to describe the situation in which one chromosome passes entirely through another one. Possible experiments that could test these theoretical analyses are discussed.