The three-dimensional (3D) structure of chromatin is intrinsically associated with gene regulation and cell function1–3. Methods based on chromatin conformation capture have mapped chromatin structures in neuronal systems such as in vitro differentiated neurons, neurons isolated through fluorescence-activated cell sorting from cortical tissues pooled from different animals and from dissociated whole hippocampi4–6. However, changes in chromatin organization captured by imaging, such as the relocation of Bdnf away from the nuclear periphery after activation7, are invisible with such approaches8. Here we developed immunoGAM, an extension of genome architecture mapping (GAM)2,9, to map 3D chromatin topology genome-wide in specific brain cell types, without tissue disruption, from single animals. GAM is a ligation-free technology that maps genome topology by sequencing the DNA content from thin (about 220 nm) nuclear cryosections. Chromatin interactions are identified from the increased probability of co-segregation of contacting loci across a collection of nuclear slices. ImmunoGAM expands the scope of GAM to enable the selection of specific cell types using low cell numbers (approximately 1,000 cells) within a complex tissue and avoids tissue dissociation2,10. We report cell-type specialized 3D chromatin structures at multiple genomic scales that relate to patterns of gene expression. We discover extensive ‘melting’ of long genes when they are highly expressed and/or have high chromatin accessibility. The contacts most specific of neuron subtypes contain genes associated with specialized processes, such as addiction and synaptic plasticity, which harbour putative binding sites for neuronal transcription factors within accessible chromatin regions. Moreover, sensory receptor genes are preferentially found in heterochromatic compartments in brain cells, which establish strong contacts across tens of megabases. Our results demonstrate that highly specific chromatin conformations in brain cells are tightly related to gene regulation mechanisms and specialized functions.
Using numerical simulations, the rheological response of an athermal assembly of soft particles with tunable attractive interactions is studied in the vicinity of jamming. At small attractions, a fragile solid develops and a finite yield stress is measured. Moreover, the measured flow curves have unstable regimes, which lead to persistent shearbanding. These features are rationalized by establishing a link between the rheology and the inter-particle connectivity, which also provides a minimal model to describe the flow curves.PACS numbers: 83.10. Rs,83.60.Wc,66.20.Cy In nature, soft disordered solids occur in different forms (eg. gels, emulsions, colloids, foams, grains etc) across a wide range of packing fractions φ, which is made possible by the tuning of particle interactions. The flow properties of these soft materials have been harnessed for various applications, e.g. in the food or the chemical industry. Thus, understanding the role of particle interactions and the corresponding mechanisms which lead to observed rheological behaviour is an important recurrent theme.For non-Brownian suspensions of frictionless repulsive spheres, it is observed that ramping up the packing fraction results in the occurrence of jamming at φ = φ J [1, 2]. The rheological signature of the onset of jamming is the development of a finite yield stress at φ J [3]. For Brownian suspensions of such particles, it has been shown that a yield stress exists at φ < φ J , due to the presence of thermal vibrations [4]. A similar systematic investigation of how the jamming paradigm is changing upon the introduction of attractive particle interactions is still missing. It is known that at smaller φ, such systems do exhibit finite yield stress [5,9,19,24]; but, a quantitative bridge with the jamming scenario needs to be developed.Such studies are also needed since shear-banding, the phenomenon of spatially inhomogeneous flows observed in many soft yield-stress fluids [6, 7], has often been attributed to attractive interactions [8,9]. In general, persistent occurrence of shear-bands has been linked to nonmontonic constitutive laws leading to flow instabilities [6, 10] (e.g. in micelles [11]). It is not known how interparticle attractions could result in such instabilities.Conceptually, one can imagine the steady flowing state to be a regime where there is a continuous competition between the rupturing induced by shear and processes that try to restore local structure. Theoretical models suggest that non-monotonic flow curves can occur due to long-lived local fluidizations when the post-rupture restructuring takes a very long time [12][13][14]. However, experiments and numerical simulations have shown that for φ > φ J , no such instabilities occur in the flow curve for either repulsive or attractive systems [15][16][17][18]. The question now arises whether for φ < φ J , a short-ranged attraction which introduces a new lengthscale for structure formation leads to longer restoration timescales and if this is indeed the origin of a shear banding ...
Loop-extrusion and phase-separation have been proposed as mechanisms that shape chromosome spatial organization. It is unclear, however, how they perform relative to each other in explaining chromatin architecture data and whether they compete or co-exist at the single-molecule level. Here, we compare models of polymer physics based on loop-extrusion and phase-separation, as well as models where both mechanisms act simultaneously in a single molecule, against multiplexed FISH data available in human loci in IMR90 and HCT116 cells. We find that the different models recapitulate bulk Hi-C and average multiplexed microscopy data. Single-molecule chromatin conformations are also well captured, especially by phase-separation based models that better reflect the experimentally reported segregation in globules of the considered genomic loci and their cell-to-cell structural variability. Such a variability is consistent with two main concurrent causes: single-cell epigenetic heterogeneity and an intrinsic thermodynamic conformational degeneracy of folding. Overall, the model combining loop-extrusion and polymer phase-separation provides a very good description of the data, particularly higher-order contacts, showing that the two mechanisms can co-exist in shaping chromatin architecture in single cells.
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