Loop extrusion by structural maintenance of chromosomes (SMC) complexes has been proposed as a mechanism to organize chromatin in interphase and metaphase. However, the requirements for chromatin organization in these cell cycle phases are different, and it is unknown whether loop extrusion dynamics and the complexes that extrude DNA also differ. Here, we used Xenopus egg extracts to reconstitute and image loop extrusion of single DNA molecules during the cell cycle. We show that loops form in both metaphase and interphase, but with distinct dynamic properties. Condensin extrudes DNA loops non-symmetrically in metaphase, whereas cohesin extrudes loops symmetrically in interphase. Our data show that loop extrusion is a general mechanism underlying DNA organization, with dynamic and structural properties that are biochemically regulated during the cell cycle.
Vitamin D signaling regulates cell proliferation and differentiation, and epidemiological data suggest that it functions as a cancer chemopreventive agent, although the underlying mechanisms are poorly understood. Vitamin D signaling can suppress expression of genes regulated by c-MYC, a transcription factor that controls epidermal differentiation and cell proliferation and whose activity is frequently elevated in cancer. We show through cell-and animal-based studies and mathematical modeling that hormonal 1,25-dihydroxyvitamin D (1,25D) and the vitamin D receptor (VDR) profoundly alter, through multiple mechanisms, the balance in function of c-MYC and its antagonist the transcriptional repressor MAD1/MXD1. 1,25D inhibited transcription of c-MYC-regulated genes in vitro, and topical 1,25D suppressed expression of c-MYC and its target setd8 in mouse skin, whereas MXD1 levels increased. 1,25D inhibited MYC gene expression and accelerated its protein turnover. In contrast, it enhanced MXD1 expression and stability, dramatically altering ratios of DNA-bound c-MYC and MXD1. Remarkably, F-box protein FBW7, an E3-ubiquitin ligase, controlled stability of both arms of the c-MYC/MXD1 push-pull network, and FBW7 ablation attenuated 1,25D regulation of c-MYC and MXD1 turnover. Additionally, c-MYC expression increased upon VDR knockdown, an effect abrogated by ablation of MYC regulator β-catenin. c-MYC levels were widely elevated in vdr −/− mice, including in intestinal epithelium, where hyperproliferation has been reported, and in skin epithelia, where phenotypes of VDR-deficient mice and those overexpressing epidermal c-MYC are similar. Thus, 1,25D and the VDR regulate the c-MYC/MXD1 network to suppress c-MYC function, providing a molecular basis for cancer preventive actions of vitamin D.V itamin D is obtained naturally from limited dietary sources. It is also generated by cutaneous conversion of 7-dehydrocholesterol in the presence of adequate surface solar UV-B radiation, which varies with latitude and time of year (1). Vitamin D has attracted broad clinical interest because insufficiency or deficiency is widespread in several populations worldwide (2-4). Although initially identified as a regulator of calcium homeostasis, vitamin D is now known to have a broad spectrum of actions, driven by the virtually ubiquitous expression of the vitamin D receptor (VDR), a nuclear receptor and hormone-regulated transcription factor. For example, it acts as a chemopreventive agent in several animal models of cancer and induces cell-cycle arrest and nonmalignant and malignant cell differentiation (5-11). Epidemiological data have provided associations between lack of UV-B exposure, vitamin D insufficiency, and the prevalence of certain cancers (12). A large prospective study associated vitamin D sufficiency with reduced total cancer incidence and mortality, particularly in digestive cancers [head and neck squamous cell carcinoma (HNSCC), esophageal, pancreatic, stomach, and colorectal cancers] and leukemias (13). VDR gene polymorphi...
Interactions between liquids and surfaces generate forces1,2 that are crucial for many processes in biology, physics and engineering, including the motion of insects on the surface of water3, modulation of the material properties of spider silk4 and self-assembly of microstructures5. Recent studies have shown that cells assemble biomolecular condensates via phase separation6. In the nucleus, these condensates are thought to drive transcription7, heterochromatin formation8, nucleolus assembly9 and DNA repair10. Here we show that the interaction between liquid-like condensates and DNA generates forces that might play a role in bringing distant regulatory elements of DNA together, a key step in transcriptional regulation. We combine quantitative microscopy, in vitro reconstitution, optical tweezers and theory to show that the transcription factor FoxA1 mediates the condensation of a protein–DNA phase via a mesoscopic first-order phase transition. After nucleation, co-condensation forces drive growth of this phase by pulling non-condensed DNA. Altering the tension on the DNA strand enlarges or dissolves the condensates, revealing their mechanosensitive nature. These findings show that DNA condensation mediated by transcription factors could bring distant regions of DNA into close proximity, suggesting that this physical mechanism is a possible general regulatory principle for chromatin organization that may be relevant in vivo.
SummaryCapillary forces are driven by interactions between liquids and surfaces1. These forces are crucial for many processes ranging from biology and physics to engineering, such as the motion of aquatic insects on the surface of water2, modulation of the material properties of spider silk3,4, and self-assembly of small objects and microstructures5. Recent studies have shown that cells assemble biomolecular condensates in a manner similar to phase separation6. In the nucleus, these condensates are thought to drive transcription7–10, heterochromatin formation11,12, nucleolus assembly13,14, and DNA repair15,16. Here, we test if the interaction between liquid-like condensates and chromatin generates capillary forces, which might play a role in bringing distant regulatory elements of DNA together, a key step in transcriptional regulation. We combine quantitative microscopy, in vitro reconstitution, and theory to show that the pioneer transcription factor FoxA1 mediates the condensation of a DNA-protein phase via a mesoscopic first-order phase transition. Surprisingly, after nucleation, capillary forces drive growth of this phase by pulling non-condensed DNA. Altering the tension on the DNA strand enlarges or dissolves the condensates, revealing their mechanosensitive nature. These findings show that DNA condensation mediated by transcription factors could bring distant regions of DNA in close proximity using capillary forces. Our work suggests that the physics of DNA and protein condensation driven by capillary forces provides a general regulatory principle for chromatin organization.
Biological, physical, and social systems often display qualitative changes in dynamics. Developing early warning signals to predict the onset of these transitions is an important goal. The current work is motivated by transitions of cardiac rhythms, where the appearance of alternating features in the timing of cardiac events is often a precursor to the initiation of serious cardiac arrhythmias. We treat embryonic chick cardiac cells with a potassium channel blocker, which leads to the initiation of alternating rhythms. We associate this transition with a mathematical instability, called a period-doubling bifurcation, in a model of the cardiac cells. Period-doubling bifurcations have been linked to the onset of abnormal alternating cardiac rhythms, which have been implicated in cardiac arrhythmias such as T-wave alternans and various tachycardias. Theory predicts that in the neighborhood of the transition, the system's dynamics slow down, leading to noise amplification and the manifestation of oscillations in the autocorrelation function. Examining the aggregates' interbeat intervals, we observe the oscillations in the autocorrelation function and noise amplification preceding the bifurcation. We analyze plots-termed return maps-that relate the current interbeat interval with the following interbeat interval. Based on these plots, we develop a quantitative measure using the slope of the return map to assess how close the system is to the bifurcation. Furthermore, the slope of the return map and the lag-1 autocorrelation coefficient are equal. Our results suggest that the slope and the lag-1 autocorrelation coefficient represent quantitative measures to predict the onset of abnormal alternating cardiac rhythms.early warning signals | period-doubling bifurcations | cardiac arrhythmias | dynamical systems
Biological systems contain biochemical control networks that reside within a remarkable spatial structure. We present a theoretical study of a biological system in which two chemically coupled species, an activating species and an inhibiting species forming a negative feedback, are synthesized at unique sites and interact with each other through diffusion. The dynamical behaviors in these systems depend on the spatial locations of these synthetic sites. In a negative feedback system with two sites, we find two dynamical modes: fixed point and stable oscillations whose frequency can be tuned by varying the distance between the sites. When there are multiple synthetic sites, we find more diverse dynamics, including chaos, quasiperiodicity, and bistability. Based on this theoretical analysis, it should be possible to create in the laboratory synthetic circuits displaying these dynamics. This study illustrates the concept of "spatial switching," in which bifurcations in the dynamics occur as a function of the geometry of the system.
Neuronal hypersynchrony is implicated in epilepsy and other diseases. The low-frequency, spatially averaged electric fields from many thousands of neurons have been shown to promote synchrony. It remains unclear whether highly transient, spatially localized electric fields from single action potentials (ephaptic coupling) significantly affect spike timing of neighboring cells and in consequence, population synchrony. In this study, we simulated the extracellular potentials and the resulting coupling between neurons in the NEURON environment and generalized their connection rules to create an oscillator network model of a sheet of ephaptically coupled neurons. With the use of both models, we explained several aspects of epileptiform behavior not previously modeled by synaptically coupled networks. Importantly, reduction of neuron spacing induced synchronization via single-spike ephaptic coupling, agreeing with seizure suppression seen clinically and in vitro via extracellular volume adjustment. Further reduction of neuron spacing yielded locally synchronized clusters, providing a mechanism for recent in vitro observations of localized neuronal synchrony in the absence of synaptic and gap-junction coupling.
Chaotic rhythms in deterministic models can arise as a consequence of changes in model parameters. We carried out experimental studies in which we induced a variety of complex rhythms in aggregates of embryonic chick cardiac cells using E-4031 (1.0-2.5 μM), a drug that blocks the hERG potassium channel. Following the addition of the drug, the regular rhythm evolved to display a spectrum of complex dynamics: irregular rhythms, bursting oscillations, doublets, and accelerated rhythms. The interbeat intervals of the irregular rhythms can be described by one-dimensional return maps consistent with chaotic dynamics. A Hodgkin-Huxley-style cardiac ionic model captured the different types of complex dynamics following blockage of the hERG mediated potassium current.
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