scholarly journals Epigenetic Transitions and Knotted Solitons in Stretched Chromatin

2017 ◽  
Author(s):  
D. Michieletto ◽  
E. Orlandini ◽  
D. Marenduzzo

The spreading and regulation of epigenetic marks on chromosomes is crucial to establish and maintain cellular identity. Nonetheless, the dynamical mechanism leading to the establishment and maintenance of a given, cell-line specific, epigenetic pattern is still poorly understood. In this work we propose, and investigate in silico, a possible experimental strategy to illuminate the interplay between 3D chromatin structure and epigenetic dynamics. We consider a set-up where a reconstituted chromatin fibre is stretched at its two ends (e.g., by laser tweezers), while epigenetic enzymes (writers) and chromatin-binding proteins (readers) are flooded into the system. We show that, by tuning the stretching force and the binding affinity of the readers for chromatin, the fibre undergoes a sharp transition between a stretched, epigenetically disordered, state and a crumpled, epigenetically coherent, one. We further investigate the case in which a knot is tied along the chromatin fibre, and find that the knotted segment enhances local epigenetic order, giving rise to “epigenetic solitons” which travel and diffuse along chromatin. Our results point to an intriguing coupling between 3D chromatin topology and epigenetic dynamics, which may be investigated via single molecule experiments.




Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 623-623
Author(s):  
Rustem I. Litvinov ◽  
Henry Shuman ◽  
Joel S. Bennett ◽  
John W. Weisel

Abstract The regulated ability of the platelet integrin αIIbβ3 to bind fibrinogen plays a crucial role in platelet aggregation and primary hemostasis. We have developed a model system based on laser tweezers that enables us to measure directly the mechanical forces needed to separate single receptor-ligand complexes. In this system, a ligand-coated bead can be trapped by the laser and repeatedly brought into contact with a receptor-coated pedestal so that the forces required to separate the two can be measured and displayed as “rupture force” histograms. We have applied this system to the interaction of fibrinogen and αIIbβ3 by measuring the rupture force required to separate a laser-trapped bead coated with fibrinogen from an immobilized pedestal coated with purified αIIbβ3. These measurements revealed that bimolecular αIIbβ3-fibrinogen interactions are characterized by rupture forces ranging from 20 pN to 150 pN. We found that the yield strength of αIIbβ3-fibrinogen interactions was independent of the rate at which force was applied over a range of 160 to 16,000 pN/s, but the frequency of fibrinogen binding to αIIbβ3 during repeated contacts correlated strongly with the duration of contact between the αIIbβ3- and fibrinogen-coated surfaces. The observed rupture forces could be segregated into small (20–40 pN), intermediate (40–60 pN), and high (>60 pN) force regimes, each of which displayed unique kinetic behavior. Thus, the contact time needed to reach half maximal fibrinogen binding at a constant loading rate of 1,600 pN/s was ~ 1 ms for the 20–40 pN, 20 ms for the 40–60 pN, and 70 ms for the >60 pN force regimes. Increasing the surface density of immobilized fibrinogen changed the probability of αIIbβ3 binding to fibrinogen >3.5-fold, but did not affect the yield strength profile, implying that these measurements represent interactions between individual molecules. Each force regime also differed in its susceptibility to the inhibitory effect of αIIbβ3 antagonists and to the activating effect of Mn2+. Thus, the low molecular weight αIIbβ3 antagonists H12 peptide, tirofiban, and RGDS were most effective in inhibiting weak interactions, whereas the monoclonal antibodies A2A9 and abciximab were most effective in inhibiting the stronger ones. In the presence of Mn2+, the strongest component of the yield force distribution increased more than 2.5-fold while the moderate force component increased only 1.5-fold. In addition, rupture forces in the range of 60 to 150 pN disappeared gradually when αIIbβ3 preparations were stored at 4°C for 7 d, suggesting that the αIIbβ3 conformation corresponding to these rupture forces is labile. Taken together, these data suggest that fibrinogen binding to αIIbβ3 is a complex, time-dependent multi-step process during which the strength of the bond between αIIbβ3 and fibrinogen appears to progressively increase.



2019 ◽  
Author(s):  
Ida S. Opstad ◽  
Florian Ströhl ◽  
Marcus Fantham ◽  
Colin Hockings ◽  
Oliver Vanderpoorten ◽  
...  

Large fields of view (FOVs) in total internal reflection fluorescence microscopy (TIRFM) via waveguides have been shown to be highly beneficial for single molecule localisation microscopy on fixed cells [1, 2] and have also been demonstrated for short-term live-imaging of robust cell types [3–5], but not yet for delicate primary neurons nor over extended periods of time. Here, we present a waveguide-based TIRFM set-up for live-cell imaging of demanding samples. Using the developed microscope, referred to as the ChipScope, we demonstrate successful culturing and imaging of fibroblasts, primary rat hippocampal neurons and axons of Xenopus retinal ganglion cells (RGC). The high contrast and gentle illumination mode provided by TIRFM coupled with the exceptionally large excitation areas and superior illumination homogeneity offered by photonic waveguides have potential for a wide application span in neuroscience applications.



Universe ◽  
2021 ◽  
Vol 7 (8) ◽  
pp. 306
Author(s):  
Jesse Daas ◽  
Wouter Oosters ◽  
Frank Saueressig ◽  
Jian Wang

We set up a consistent background field formalism for studying the renormalization group (RG) flow of gravity coupled to Nf Dirac fermions on maximally symmetric backgrounds. Based on Wetterich’s equation, we perform a detailed study of the resulting fixed point structure in a projection including the Einstein–Hilbert action, the fermion anomalous dimension, and a specific coupling of the fermion bilinears to the spacetime curvature. The latter constitutes a mass-type term that breaks chiral symmetry explicitly. Our analysis identified two infinite families of interacting RG fixed points, which are viable candidates to provide a high-energy completion through the asymptotic safety mechanism. The fixed points exist for all values of Nf outside of a small window situated at low values Nf and become weakly coupled in the large Nf-limit. Symmetry-wise, they correspond to “quasi-chiral” and “non-chiral” fixed points. The former come with enhanced predictive power, fixing one of the couplings via the asymptotic safety condition. Moreover, the interplay of the fixed points allows for cross-overs from the non-chiral to the chiral fixed point, giving a dynamical mechanism for restoring the symmetry approximately at intermediate scales. Our discussion of chiral symmetry breaking effects provides strong indications that the topology of spacetime plays a crucial role when analyzing whether quantum gravity admits light chiral fermions.



eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Edward J Banigan ◽  
Leonid A Mirny

Chromosome compaction is essential for reliable transmission of genetic information. Experiments suggest that ∼1000-fold compaction is driven by condensin complexes that extrude chromatin loops, by progressively collecting chromatin fiber from one or both sides of the complex to form a growing loop. Theory indicates that symmetric two-sided loop extrusion can achieve such compaction, but recent single-molecule studies (Golfier et al., 2020) observed diverse dynamics of condensins that perform one-sided, symmetric two-sided, and asymmetric two-sided extrusion. We use simulations and theory to determine how these molecular properties lead to chromosome compaction. High compaction can be achieved if even a small fraction of condensins have two essential properties: a long residence time and the ability to perform two-sided (not necessarily symmetric) extrusion. In mixtures of condensins I and II, coupling two-sided extrusion and stable chromatin binding by condensin II promotes compaction. These results provide missing connections between single-molecule observations and chromosome-scale organization.



2010 ◽  
Vol 98 (3) ◽  
pp. 184a
Author(s):  
Catherine Tardin ◽  
Manoel Manghi ◽  
Julien Baglio ◽  
Laurence Salome ◽  
Nicolas Destainville


2020 ◽  
Author(s):  
Dominik Pfennig ◽  
Andreas Albrecht ◽  
Julia Nowak ◽  
Peter Jomo Walla

AbstractIn the past, different methods have been presented to determine the 3D orientation of single molecules in a microscopic set-up by excitation polarization modulation. Using linearly polarized illumination from different directions and thereby measuring different 2D projections enables reconstructing the full 3D orientation. Theoretically, two projections suffice for a full 3D orientation determination if the intensities are properly calibrated. If they are not, a third projection will enable unambiguous orientation measurements. The question arises if three projections already contain the maximum information on the 3D orientation when also considering the limited number of available photons and shot noise in an experiment, or if detecting more projections or even continuously changing the projection direction during a measurement provides more information with an identical number of available photons. To answer this principle question, we constructed a simple device allowing for exploring any projection direction available with a particular microscope objective and tested several different excitation modulation schemes using simulated as well as experimental single molecule data. We found that three different projections in fact already do provide the maximum information also for noisy data. Our results do not indicate a significant improvement in angular precision in comparison to three projections, both when increasing the number of projections and when modulating the projection direction and polarization simultaneously during the measurement.In fluorescence microscopy polarized illumination from different directions enables the determination of the 3D orientation of single molecules by combining the 2D information of different projection directions. Ambiguities that emerge when using only two projections can be eliminated using a third projection. In a systematic study we show that – also considering the limited number of available photons and shot noise in an experiment – three projection directions already contain the maximum information on the 3D orientation. Our results do not indicate a significant improvement in angular precision in comparison to three projections, both when increasing the number of projections and when modulating the projection direction and polarization simultaneously during the measurement.



2020 ◽  
Author(s):  
Edward J. Banigan ◽  
Leonid A. Mirny

AbstractCompaction of chromosomes is essential for reliable transmission of genetic information. Experiments suggest that this ∼ 1000-fold compaction is driven by condensin complexes that extrude chromatin loops, i.e., progressively collect chromatin fiber from one or both sides of the complex to form a growing loop. Theory indicates that symmetric two-sided loop extrusion can achieve such compaction, but recent single-molecule studies observed diverse dynamics of condensins that perform one-sided, symmetric two-sided, and asymmetric two-sided extrusion.We use simulations and theory to determine how these molecular properties lead to chromosome compaction. High compaction can be achieved if even a small fraction of condensins have two essential properties: a long residence time and the ability to perform two-sided (not necessarily symmetric) extrusion. In mixtures of condensins I and II, coupling of two-sided extrusion and stable chromatin binding by condensin II promotes compaction. These results provide missing connections between single-molecule observations and chromosome-scale organization.



Author(s):  
Kirti Prakash

We report that high-density single-molecule super-resolution microscopy can be achieved with a conventional epifluorescence microscope set-up and a mercury arc lamp. The configuration termed as laser-free super-resolution microscopy (LFSM) is an extension of single-molecule localization microscopy (SMLM) techniques and allows single molecules to be switched on and off (a phenomenon termed as ‘blinking’), detected and localized. The use of a short burst of deep blue excitation (350–380 nm) can be further used to reactivate the blinking, once the blinking process has slowed or stopped. A resolution of 90 nm is achieved on test specimens (mouse and amphibian meiotic chromosomes). Finally, we demonstrate that stimulated emission depletion and LFSM can be performed on the same biological sample using a simple commercial mounting medium. It is hoped that this type of correlative imaging will provide a basis for a further enhanced resolution. This article is part of the Theo Murphy meeting issue ‘Super-resolution structured illumination microscopy (part 1)’.



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