Topological gelation of reconnecting polymers.

DNA recombination is a ubiquitous process that ensures genetic diversity. Contrary to textbook pictures, DNA recombination, as well as generic DNA translocations, occurs in a confined and highly entangled environment. Inspired by this observation, here, we investigate a solution of semiflexible polymer rings undergoing generic cutting and reconnection operations under spherical confinement. Our setup may be realized using engineered DNA in the presence of recombinase proteins or by considering micelle-like components able to form living (or reversibly breakable) polymer rings. We find that in such systems, there is a topological gelation transition, which can be triggered by increasing either the stiffness or the concentration of the rings. Flexible or dilute polymers break into an ensemble of short, unlinked, and segregated rings, whereas sufficiently stiff or dense polymers self-assemble into a network of long, linked, and mixed loops, many of which are knotted. We predict that the two phases should behave qualitatively differently in elution experiments monitoring the escape dynamics from a permeabilized container. Besides shedding some light on the biophysics and topology of genomes undergoing DNA reconnection in vivo, our findings could be leveraged in vitro to design polymeric complex fluids-e.g., DNA-based complex fluids or living polymer networks-with desired topologies.

Topological Spectra and Entropy of Chromatin Loop Networks.

The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fiber is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors and RNA polymerases. This physical model leads to the natural emergence of clusters of proteins and binding sites, accompanied by the folding of chromatin into a set of topologies, each associated with a different network of loops. Here, we combine numerics and analytics to first classify these networks and then find their relative importance or statistical weight, when the properties of the underlying polymer are those relevant to chromatin. Unlike polymer networks previously studied, our chromatin networks have finite average distances between successive binding sites, and this leads to giant differences between the weights of topologies with the same number of edges and nodes but different wiring. These weights strongly favor rosettelike structures with a local cloud of loops with respect to more complicated nonlocal topologies. Our results suggest that genes should overwhelmingly fold into a small fraction of all possible 3D topologies, which can be robustly characterized by the framework we propose here.

Condensin extrudes DNA loops in steps up to hundreds of base pairs that are generated by ATP binding events.

The condensin SMC protein complex organizes chromosomal structure by extruding loops of DNA. Its ATP-dependent motor mechanism remains unclear but likely involves steps associated with large conformational changes within the ∼50 nm protein complex. Here, using high-resolution magnetic tweezers, we resolve single steps in the loop extrusion process by individual yeast condensins. The measured median step sizes range between 20-40 nm at forces of 1.0-0.2 pN, respectively, comparable with the holocomplex size. These large steps show that, strikingly, condensin typically reels in DNA in very sizeable amounts with ∼200 bp on average per single extrusion step at low force, and occasionally even much larger, exceeding 500 bp per step. Using Molecular Dynamics simulations, we demonstrate that this is due to the structural flexibility of the DNA polymer at these low forces. Using ATP-binding-impaired and ATP-hydrolysis-deficient mutants, we find that ATP binding is the primary step-generating stage underlying DNA loop extrusion. We discuss our findings in terms of a scrunching model where a stepwise DNA loop extrusion is generated by an ATP-binding-induced engagement of the hinge and the globular domain of the SMC complex.

Three-dimensional loop extrusion.

Loop extrusion convincingly describes how certain structural maintenance of chromosome (SMC) proteins mediate the formation of large DNA loops. Yet most of the existing computational models cannot reconcile recent in vitro observations showing that condensins can traverse each other, bypass large roadblocks, and perform steps longer than their own size. To fill this gap, we propose a three-dimensional (3D) "trans-grabbing" model for loop extrusion, which not only reproduces the experimental features of loop extrusion by one SMC complex but also predicts the formation of so-called Z-loops via the interaction of two or more SMCs extruding along the same DNA substrate. By performing molecular dynamics simulations of this model, we discover that the experimentally observed asymmetry in the different types of Z-loops is a natural consequence of the DNA tethering in vitro. Intriguingly, our model predicts this bias to disappear in the absence of tethering and a third type of Z-loop, which has not yet been identified in experiments, to appear. Our model naturally explains roadblock bypassing and the appearance of steps larger than the SMC size as a consequence of non-contiguous DNA grabbing. Finally, this study is the first, to our knowledge, to address how Z-loops and bypassing might occur in a way that is broadly consistent with existing cis-only 1D loop extrusion models.

Combinatorics and topological weights of chromatin loop networks.

Polymer physics models suggest that chromatin spontaneously folds into loop networks with transcription units (TUs), such as enhancers and promoters, as anchors. Here we use combinatoric arguments to enumerate the emergent chromatin loop networks, both in the case where TUs are labeled and where they are unlabeled. We then combine these mathematical results with those of computer simulations aimed at finding the inter-TU energy required to form a target loop network. We show that different topologies are vastly different in terms of both their combinatorial weight and energy of formation. We explain the latter result qualitatively by computing the topological weight of a given network-i.e., its partition function in statistical mechanics language-in the approximation where excluded volume interactions are neglected. Our results show that networks featuring local loops are statistically more likely with respect to networks including more nonlocal contacts. We suggest our classification of loop networks, together with our estimate of the combinatorial and topological weight of each network, will be relevant to catalog three-dimensional structures of chromatin fibers around eukaryotic genes, and to estimate their relative frequency in both simulations and experiments.

Bridging-induced phase separation induced by cohesin SMC protein complexes.

Structural maintenance of chromosome (SMC) protein complexes are able to extrude DNA loops. While loop extrusion constitutes a fundamental building block of chromosomes, other factors may be equally important. Here, we show that yeast cohesin exhibits pronounced clustering on DNA, with all the hallmarks of biomolecular condensation. DNA-cohesin clusters exhibit liquid-like behavior, showing fusion of clusters, rapid fluorescence recovery after photobleaching and exchange of cohesin with the environment. Strikingly, the in vitro clustering is DNA length dependent, as cohesin forms clusters only on DNA exceeding 3 kilo-base pairs. We discuss how bridging-induced phase separation, a previously unobserved type of biological condensation, can explain the DNA-cohesin clustering through DNA-cohesin-DNA bridges. We confirm that, in yeast cells in vivo, a fraction of cohesin associates with chromatin in a manner consistent with bridging-induced phase separation. Biomolecular condensation by SMC proteins constitutes a new basic principle by which SMC complexes direct genome organization.

Desynapsis and precocious cytokinesis in Brachiaria humidicola (Poaceae) compromise meiotic division.

The forage grass species Brachiaria humidicola is native to African savannas. Owing to its good adaptation to poorly drained and infertile acid soils, it has achieved wide utilization for pastures in Brazilian farms. Among the 55 accessions of B. humidicola analysed from the Embrapa Beef Cattle collection, one (H022), presented desynapsis and an abnormal pattern of cytokinesis in the first meiotic division. Among 28 inflorescences analysed in this accession, 12 were affected by the anomaly. In affected meiocytes, the first cytokinesis occurred in metaphase I and was generally perpendicular to a wide-metaphase plate, dividing the genome into two parts with an equal or unequal number of chromosomes. The normal cytokinesis after telophase I did not occur, and the meiocytes entered metaphase II, progressing to the end of meiosis with the occurrence of the second cytokinesis. As the first cytokinesis occurred precociously, whereas the second was normal, tetrads were formed but with unbalanced chromosome numbers in microspores. Abnormal cytokinesis occurred only in those meiocytes that underwent desynapsis after diakinesis. The implications of this abnormality in the Brachiaria breeding programme are discussed.

The role of the peroxisome proliferator-activated receptor-alpha (PPAR-alpha) in the regulation of acute inflammation.

The peroxisome proliferator-activated receptor-alpha (PPAR-alpha) is a member of the nuclear receptor superfamily of ligand-dependent transcription factors related to retinoid, steroid, and thyroid hormone receptors. The aim of the present study was to evaluate the role of the PPAR-alpha receptor on the development of acute inflammation. To address this question, we used two animal models of acute inflammation (carrageenan-induced paw edema and carrageenan-induced pleurisy). We report here that when compared with PPAR-alpha wild-type mice, PPAR-alpha knockout mice (PPAR-alphaKO) mice experienced a higher rate of the extent and severity when subjected to carrageenan injection in the paw edema model or to carrageenan administration in the pleurisy model. In particular, the absence of a functional PPAR-alpha gene in PPAR-alphaKO mice resulted in a significant augmentation of various inflammatory parameters (e.g., enhancement of paw edema, pleural exudate formation, mononuclear cell infiltration, and histological injury) in vivo. Furthermore, the absence of a functional PPAR-alpha gene enhanced the staining (immunohistochemistry) for FAS ligand in the paw and in the lung and the expression of tumor necrosis factor alpha and interleukin-1beta in the lungs of carrageenan-treated mice. In conclusion, the increased inflammatory response observed in PPAR-alphaKO mice strongly suggests that a PPAR-alpha pathway modulates the degree of acute inflammation in the mice.

Combining dendritic cells and B cells for presentation of oxidised tumour antigens to CD8+ T cells.

The dendritic cell (DC) is the foremost antigen-presenting cell (APC) for ex vivo expansion of tumour-specific patient T cells. Despite marked responses in some patients following reinfusion of DC-activated autologous or HLA-matched donor T cells, overall response rates remain modest in solid tumours. Furthermore, most studies aim to generate immune responses against defined tumour-associated antigens (TAA), however, meta-analysis reveals that those approaches have less clinical success than those using whole tumour cells or their components. Tumour lysate (TL) is used as a source of tumour antigen in clinical trials and potentially represents the full range of TAAs in an undefined state. Little is known about how different APCs cooperate to present TL antigens. We examined the effect of oxidised whole-cell lysate (ox-L) versus soluble fraction freeze-thaw lysate (s-L) on bone marrow-derived DCs and macrophages, and magnetic bead-isolated splenic B cells. The APCs were used individually, or in combination, to prime T cells. CD8+ T cells produced interferon (IFN)-γ in response to both s-L and ox-L, but only proliferated in response to ox-L. IFN-γ production and proliferation was enhanced by priming with the DC+B cell combination. Compared to DC alone, a trend toward greater interleukin (IL)-12 production was observed when DC+B cell were loaded with s-L and ox-L antigens. CD8+ T-cell specific lysis in vivo was greatest in ox-L-primed groups and DC+B cell priming significantly increased in vivo cytotoxicity compared to DC alone. These improved T-cell responses with two APCs and stressed cell lysate has implications for APC-based adoptive cell therapies.

Chromosome numbers and meiotic analysis in the pre-breeding of Brachiaria decumbens (Poaceae).

A total of 44 accessions of Brachiaria decumbens were analysed for chromosome count and meiotic behaviour in order to identify potential progenitors for crosses. Among them, 15 accessions presented 2n = 18; 27 accessions, 2n = 36; and 2 accessions, 2n = 45 chromosomes. Among the diploid accessions, the rate of meiotic abnormalities was low, ranging from 0.82% to 7.93%. In the 27 tetraploid accessions, the rate of meiotic abnormalities ranged from 18.41% to 65.83%. The most common meiotic abnormalities were related to irregular chromosome segregation, but chromosome stickiness and abnormal cytokinesis were observed in low frequency. All abnormalities can compromise pollen viability by generating unbalanced gametes. Based on the chromosome number and meiotic stability, the present study indicates the apomictic tetraploid accessions that can act as male genitor to produce interspecific hybrids with B. ruziziensis or intraspecific hybrids with recently artificially tetraploidized accessions.

Unusual cytological patterns of microsporogenesis in Brachiaria decumbens: abnormalities in spindle and defective cytokinesis causing precocious cellularization.

Cytogenetic studies carried out in the tetraploid accession BRA001068 of Brachiaria decumbens, also known as cv. Basilisk, revealed an unusual pattern of microsporogenesis. The spindle in metaphase I and anaphase I became heavily stained with propionic carmine. In telophase I, the interzonal microtubules continued to be intensely stained, and during the phragmoplast formation the fibers were pushed to the cell wall, persisting until prophase II, even after cytokinesis. Due to its tetraploid condition, the accession presented many cells with precocious chromosome migration to the poles in metaphase I and laggards in anaphase I that gave rise to micronuclei in telophase I. While in other polyploid accessions of Brachiaria micronuclei remained in this condition until the second cytokinesis, the micronuclei in this accession organized their own spindle in the second division. In several microsporocytes, the micronuclei with their minispindle were divided further into microcytes by additional cytokinesis. Some curious planes of cytokinesis were found in some cells, with partitioning of cytoplasm into cells of irregular shape. The result consisted of a high frequency of abnormal products of meiosis. Quadrivalents were observed in diakinesis at low frequency, which suggests a segmental allotetraploid and the inability of both genomes to co-ordinate their activities, leading to multiple spindle and precocious cellularization. In spite of abnormal meiotic products reducing pollen fertility, seed production was normal. Enough normal pollen was available to fertilize the central-cell nucleus of the embryo sac and produce normal endosperm in this pseudogamous aposporous apomictic accession.

Absence of microspore polarity, symmetric divisions and pollen cell fate in Brachiaria decumbens (Gramineae).

Meiotic division and male gametophyte development were analyzed in one tetraploid (2n = 4x = 36) accession of Brachiaria decumbens cv. Basilisk that showed some pollen sterility. Meiotic process was typical of polyploids in that it consisted of multiple chromosome associations. Precocious chromosome migration to the poles, laggards, and micronucleus formation were abundant in both meiosis I and II and resulted in tetrads with micronuclei. After callose dissolution, microspores were released into the anther locule and had the semblance of being normal. Although each microspore initiated its differentiation by pollen mitosis, in 43.24% of the microspores, nuclear polarization was not observed and the typical hemispherical cell plate was not detected. Division was symmetric and microspores lacked differentiation between the vegetative and the generative cell. Both nuclei were of equal size, presented equal chromatin condensation, and had a spherical shape. After the first pollen mitosis and cytokinesis, each cell underwent a new symmetric mitosis without nuclear polarization. At the end of the second pollen mitosis, four equal nuclei were observed in each pollen grain. After the second cytokinesis, the cells gave rise to four equal-sized pollen grains with a similar tetrad configuration that initially remained together. Sterile pollen grains resulted from abnormal pollen mitosis. This anomaly may be explained by a mutation, probably affecting microtubule cytoskeleton formation. The importance of this male-sterile mutation for Brachiaria breeding programs is discussed.

Meiotic arrest compromises pollen fertility in an interspecific hybrid between Brachiaria ruziziensis x Brachiaria decumbens (Poaceae: paniceae)

Microsporogenesis was analyzed in an interspecific hybrid between an artificially tetraploidized sexual accession of Brachiaria ruziziensis (2n=4x=36) and a natural apomictic tetraploid accession of B. decumbens. Syncytes involving a large number of cells were recorded in 15.4 percent of meiocytes. Meiosis progressed normally in syncytes during prophase I; in metaphase I, however, several nuclei were found fusioned, showing chromosome stickiness and several chromosome fragments. Meiosis was arrested in metaphase I and pycnotic nuclei and micronuclei were formed. Abnormal cytokinesis fractionated the syncyte into abnormal meiotic products that were covered by the pollen wall. Meiocytes in leptotene were recorded in all the slides prepared for both meiotic divisions, and abnormal "pollen grains" with well-developed pollen wall but containing leptotene nuclei were recorded in 9.18 percent of grains analyzed. These findings suggested that the meiocytes received the signal to enter meiosis but lacked the signal to proceed beyond leptotene. Despite the absence of the meiotic process, such cells were covered by pollen grain wall. Total pollen sterility resulted from these abnormalities combined with still others observed among meiocytes.

A microsporogênese de um híbrido interespecífico entre um acesso sexual tetraploidizado artificialmente de Brachiaria ruziziensis (2n=4x=36) e um acesso apomítico tetraplóide natural de B. decumbens (2n=4x=36) foi analisada. Sincícios envolvendo um grande número de células foram encontrados em 15,40 por cento dos meiócitos. A meiose progrediu normalmente nos sincícios durante a prófase I; em metáfase I, todavia, muitos núcleos fundiram-se, mostrando ainda aderências cromossômicas e inúmeros fragmentos. O processo meiótico foi interrompido na metáfase I, quando a cromatina formou núcleos picnóticos. Citocineses anormais fracionaram os sincícios em produtos meióticos anômalos que foram recobertos pela parede do grão de pólen. Meiócitos em leptóteno também foram observados durante todo o processo meiótico e grãos de pólen anormais com parede de pólen bem desenvolvida, mas contendo núcleos leptotênicos, foram observados em 9,18 por cento dos grãos de pólen analisados. Os resultados sugerem que os meiócitos receberam o sinal para entrar em meiose, mas não receberam o sinal para prosseguir além do leptóteno. Apesar da ausência de processo meiótico completo, os meiócitos foram cobertos pela parede do grão de pólen. Estas anormalidades, combinadas com outras causadas pela poliploidia, resultaram em total esterilidade de pólen.

Abnormal spindle orientation during microsporogenesis in an interspecific Brachiaria ( Gramineae ) hybrid

This paper reports a case of abnormal spindle orientation during microsporogenesis in an interspecific hybrid of the tropical grass Brachiaria. In the affected plant, prophase I was normal. In metaphase I, bivalents were regularly co-oriented but distantly positioned and spread over the equatorial plate. In anaphase I, chromosomes failed to converge into focused poles due to parallel spindle fibers. As a consequence, in telophase I, an elongated nucleus or several micronuclei were observed in each pole. In the second division, the behavior was the same, leading to polyads with several micronuclei. A total of 40 percent of meiotic products were affected. The use of this hybrid in production systems needing good-quality seeds is discussed.

Cytogenetic evidence for genome elimination during microsporogenesis in interspecific hybrid between Brachiaria ruziziensis and B. brizantha (Poaceae)

Microsporogenesis was analyzed in an interspecific hybrid between an artificially tetraploidized sexual accession of Brachiaria ruziziensis (R genome) and a natural apomictic tetraploid accession of B. brizantha (B genome). Chromosomes associated predominantly as bivalents. From this phase to the end of meiosis, chromosomes presented irregular segregation and abnormal arrangement in the metaphase plate. During metaphase I, in 27.8 percent of meiocytes, bivalents were distributed in two metaphase plates. In anaphase I, two distinct and typical bipolar spindles were formed. In 29.7 percent of pollen mother cells, one genome did not divide synchronically, with chromosomes lagging behind or not segregating at all. The second division was very irregular, resulting in polyads. Based on previous results from analysis of a triploid hybrid between these species, where the R genome was eliminated by asynchrony during meiosis, it is suggested that the laggard genome in this hybrid also belongs to B. ruziziensis.

Chromosome numbers and meiotic behavior of some Paspalum accessions

Chromosome number and meiotic behavior were evaluated in 36 Brazilian accessions of the grass Paspalum (which had never previously been analyzed) to determinate which accessions might be useful in interspecific hybridizations. The analysis showed that one accession of Paspalum coryphaeum was diploid (2n = 2x = 20) and one accession of Paspalum conspersum hexaploid (2n = 6x = 60), the remaining 34 accessions being tetraploid (2n = 4x = 40). The pairing configuration was typical for the ploidy level i.e. in the diploid, chromosomes paired as 10 bivalents, in tetraploids as bi-, tri- and quadrivalents, and in hexaploid as 30 bivalents. A low frequency of meiotic abnormalities (less than 10%) was observed in the diploid, hexaploid and some tetraploid accessions, although the majority of tetraploid accessions showed a high frequency of meiotic irregularities. The use of accessions with a low frequency of meiotic abnormalities in breeding programs is discussed

Normal microspore production after cell fusion in Brachiaria jubata (Gramineae)

Cytogenetic studies were carried out on 22 accessions of Brachiaria jubata from the Embrapa Beef Cattle Brachiaria collection. One accession was diploid (2n = 2x = 18) and the remaining 21 were tetraploid (2n = 4x = 36). Among five tetraploid accessions, a specific and constant pattern of cell fusion involving only two microsporocytes was recorded. Meiosis proceeded normally from prophase I to the end, giving rise to an octad with normal microspores that developed into fertile pollen grains. Regular octad formation was possible because each cellular chromosome set was maintained in its proper domain, spindles were correctly positioned, and cytokinesis planes were formed in the correct places. Such behavior of meiosis in syncytes has never been reported in any other plant species.