scholarly journals Heterochromatin drives organization of conventional and inverted nuclei

2018 ◽  
Author(s):  
Martin Falk ◽  
Yana Feodorova ◽  
Natasha Naumova ◽  
Maxim Imakaev ◽  
Bryan R. Lajoie ◽  
...  
Keyword(s):  
Phase Separation ◽  
Morphological Changes ◽  
Nuclear Organization ◽  
Nuclear Periphery ◽  
Nuclear Architecture ◽  
Default State ◽  
Genomic Regions ◽  
Universal Mechanism

AbstractThe mammalian cell nucleus displays a remarkable spatial segregation of active euchromatic from inactive heterochromatic genomic regions. In conventional nuclei, euchromatin is localized in the nuclear interior and heterochromatin at the nuclear periphery. In contrast, rod photoreceptors in nocturnal mammals have inverted nuclei, with a dense heterochromatic core and a thin euchromatic outer shell. This inverted architecture likely converts rod nuclei into microlenses to facilitate nocturnal vision, and may relate to the absence of particular proteins that tether heterochromatin to the lamina. However, both the mechanism of inversion and the role of interactions between different types of chromatin and the lamina in nuclear organization remain unknown. To elucidate this mechanism we performed Hi-C and microscopy on cells with inverted nuclei and their conventional counterparts. Strikingly, despite the inversion evident in microscopy, both types of nuclei display similar Hi-C maps. To resolve this paradox we developed a polymer model of chromosomes and found a universal mechanism that reconciles Hi-C and microscopy for both inverted and conventional nuclei. Based solely on attraction between heterochromatic regions, this mechanism is sufficient to drive phase separation of euchromatin and heterochromatin and faithfully reproduces the 3D organization of inverted nuclei. When interactions between heterochromatin and the lamina are added, the same model recreates the conventional nuclear organization. To further test our models, we eliminated lamina interactions in models of conventional nuclei and found that this triggers a spontaneous process of inversion that qualitatively reproduces the pathway of morphological changes during nuclear inversion in vivo. Together, our experiments and modeling suggest that interactions among heterochromatic regions are central to phase separation of the active and inactive genome in inverted and conventional nuclei, while interactions with the lamina are essential for building the conventional architecture from these segregated phases. Ultimately our data suggest that an inverted organization constitutes the default state of nuclear architecture.

scholarly journals Rapid Magneto-Sonoporation of Adipose-Derived Cells

Materials ◽  
2021 ◽  
Vol 14 (17) ◽  
pp. 4877
Author(s):  
Miriam Filippi ◽  
Boris Dasen ◽  
Arnaud Scherberich
Keyword(s):  
Stem Cells ◽  
Tissue Repair ◽  
Morphological Changes ◽  
Adipose Derived Stem Cells ◽  
Resonance Imaging ◽  
Membrane Resealing ◽  
First Time ◽  
Stimulation Of

By permeabilizing the cell membrane with ultrasound and facilitating the uptake of iron oxide nanoparticles, the magneto-sonoporation (MSP) technique can be used to instantaneously label transplantable cells (like stem cells) to be visualized via magnetic resonance imaging in vivo. However, the effects of MSP on cells are still largely unexplored. Here, we applied MSP to the widely applicable adipose-derived stem cells (ASCs) for the first time and investigated its effects on the biology of those cells. Upon optimization, MSP allowed us to achieve a consistent nanoparticle uptake (in the range of 10 pg/cell) and a complete membrane resealing in few minutes. Surprisingly, this treatment altered the metabolic activity of cells and induced their differentiation towards an osteoblastic profile, as demonstrated by an increased expression of osteogenic genes and morphological changes. Histological evidence of osteogenic tissue development was collected also in 3D hydrogel constructs. These results point to a novel role of MSP in remote biophysical stimulation of cells with focus application in bone tissue repair.

Erastin induces ferroptosis via ferroportin-mediated iron accumulation in endometriosis

2020 ◽  
Author(s):  
Yajie Li ◽  
Xinliu Zeng ◽  
Dingheng Lu ◽  
Minuo Yin ◽  
Meirong Shan ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Lipid Peroxidation ◽  
Cell Viability ◽  
Stromal Cells ◽  
Morphological Changes ◽  
Iron Accumulation ◽  
Blue Staining ◽  
Endometrial Stromal Cells

Abstract STUDY QUESTION Could erastin activate ferroptosis to regress endometriotic lesions? SUMMARY ANSWER Erastin could induce ferroptosis to regress endometriotic lesions in endometriosis. WHAT IS KNOWN ALREADY Ectopic endometrial stromal cells (EESCs) are in an iron overloading microenvironment and tend to be more sensitive to oxidative damage. The feature of erastin-induced ferroptosis is iron-dependent accumulation of lethal lipid reactive oxygen species (ROS). STUDY DESIGN, SIZE, DURATION Eleven patients without endometriosis and 21 patients with endometriosis were recruited in this study. Primary normal and ectopic endometrial stromal cells were isolated, cultured and subjected to various treatments. The in vivo study involved 10 C57BL/6 female mice to establish the model of endometriosis. PARTICIPANTS/MATERIALS, SETTING, METHODS The markers of ferroptosis were assessed by cell viability, lipid peroxidation level and morphological changes. The cell viability was measured by colorimetric method, lipid peroxidation levels were measured by flow cytometry, and morphological changes were observed by transmission electron microscopy. Immunohistochemistry and western blot were used to detect ferroportin (FPN) expression. Prussian blue staining and immunofluorescent microscopy of catalytic ferrous iron were semi-quantified the levels of iron. Adenovirus-mediated overexpression and siRNA-mediated knockdown were used to investigate the role of FPN on erastin-induced ferroptosis in EESCs. MAIN RESULTS AND THE ROLE OF CHANCE EESCs were more susceptible to erastin treatment, compared to normal endometrial stromal cells (NESCs) (P<0.05). Treatment of cultured EESCs with erastin dramatically increased the total ROS level (P<0.05, versus control), lipid ROS level (P<0.05, versus NESCs) and intracellular iron level (P<0.05, versus NESCs). The cytotoxicity of erastin could be attenuated by iron chelator, deferoxamine (DFO), and ferroptosis inhibitors, ferrostatin-1 and liproxstatin-1, (P<0.05, versus erastin) in EESCs. In EESCs with erastin treatment, shorter and condensed mitochondria were observed by electron microscopy. These findings together suggest that erastin is capable to induce EESC death by ferroptosis. However, the influence of erastin on NESCs was slight. The process of erastin-induced ferroptosis in EESCs accompanied iron accumulation and decreased FPN expression. The overexpression of FPN ablated erastin-induced ferroptosis in EESCs. In addition, knockdown of FPN accelerated erastin-induced ferroptosis in EESCs. In a mouse model of endometriosis, we found ectopic lesions were regressed after erastin administration. LARGE SCALE DATA N/A LIMITATIONS, REASONS FOR CAUTION This study was mainly conducted in primary human endometrial stromal cells. Therefore, the function of FPN in vivo need to be further investigated. WIDER IMPLICATIONS OF THE FINDINGS Our findings reveal that erastin may serve as a potential therapeutic treatment for endometriosis. STUDY FUNDING/COMPETING INTEREST(S) This research did not receive any specific grant from funding agencies in the public, commercial or not-for-profit sectors. The authors declare no conflict of interest.

Vacuolar convolution: possible mechanisms and role of phosphatidylinositol 3,5-bisphosphate

2017 ◽  
Vol 44 (8) ◽  
pp. 751 ◽  
Author(s):  
Vadim Pérez Koldenkova ◽  
Noriyuki Hatsugai
Keyword(s):  
Morphological Changes ◽  
Stomatal Closure ◽  
Plant Cells ◽  
Reversible Transformation ◽  
Large Central Vacuole ◽  
Cellular Integrity ◽  
Lytic Vacuole ◽  
Cellular Cytoskeleton

The central or lytic vacuole is the largest intracellular organelle in plant cells, but we know unacceptably little about the mechanisms regulating its function in vivo. The underlying reasons are related to difficulties in accessing this organelle without disrupting the cellular integrity and to the dynamic morphology of the vacuole, which lacks a defined structure. Among such morphological changes, vacuolar convolution is probably the most commonly observed event, reflected in the (reversible) transformation of a large central vacuole into a structure consisting of interconnected bubbles of a smaller size. Such behaviour is observed in plant cells subjected to hyperosmotic stress but also takes place in physiological conditions (e.g. during stomatal closure). Although vacuolar convolution is a relatively common phenomenon in plants, studies aimed at elucidating its execution mechanisms are rather scarce. In the present review, we analyse the available evidence on the participation of the cellular cytoskeleton and ion transporters in vacuolar morphology dynamics, putting special emphasis on the available evidence of the role played by phosphatidylinositol 3,5-bisphosphate in this process.

scholarly journals Proteasome activity is required for the stage-specific transformation of a protozoan parasite.

1996 ◽  
Vol 184 (5) ◽  
pp. 1909-1918 ◽  
Author(s):  
J González ◽  
F J Ramalho-Pinto ◽  
U Frevert ◽  
J Ghiso ◽  
S Tomlinson ◽  
...  
Keyword(s):  
Essential Role ◽  
Morphological Changes ◽  
Protozoan Parasite ◽  
Eukaryotic Cells ◽  
Cysteine Proteinases ◽  
Axenic Medium ◽  
Cytoplasmic Proteins ◽  
Intracellular Parasites

A prominent feature of the life cycle of intracellular parasites is the profound morphological changes they undergo during development in the vertebrate and invertebrate hosts. In eukaryotic cells, most cytoplasmic proteins are degraded in proteasomes. Here, we show that the transformation in axenic medium of trypomastigotes of Trypanosoma cruzi into amastigote-like organisms, and the intracellular development of the parasite from amastigotes into trypomastigotes, are prevented by lactacystin, or by a peptide aldehyde that inhibits proteasome function. Clasto-lactacystin, an inactive analogue of lactacystin, and cell-permeant peptide aldehyde inhibitors of T. cruzi cysteine proteinases have no effect. We have also identified the 20S proteasomes from T. cruzi as a target of lactacystin in vivo. Our results document the essential role of proteasomes in the stage-specific transformation of a protozoan.

scholarly journals Paraspeckles: Paragons of functional aggregation

2015 ◽  
Vol 210 (4) ◽  
pp. 527-528 ◽  
Author(s):  
Edward Courchaine ◽  
Karla M. Neugebauer
Keyword(s):  
Gene Expression ◽  
Phase Separation ◽  
Low Complexity ◽  
Nuclear Body ◽  
Liquid Droplets ◽  
Cell Biol

Low-complexity proteins undergo phase separation in vitro, forming hydrogels or liquid droplets. Whether these form in vivo, and under what conditions, is still unclear. In this issue, Hennig et al. (2015. J. Cell Biol. http://dx.doi.org/10.1083/jcb.201504117) show that formation of the paraspeckle, a nuclear body that regulates gene expression, requires low-complexity prion-like domains (PLDs) within paraspeckle proteins. The same proteins were shown to form hydrogels, shedding light on the role of “functional aggregation” in nuclear substructure.

scholarly journals Modeling and live imaging of mechanical instabilities in the zebrafish aorta during hematopoiesis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dmitrii Chalin ◽  
Charlotte Bureau ◽  
Andrea Parmeggiani ◽  
Sergei Rochal ◽  
Karima Kissa ◽  
...  
Keyword(s):  
Morphological Changes ◽  
Axial Stress ◽  
Micromechanical Model ◽  
Model Organism ◽  
Complex Interplay ◽  
Hematopoietic Stem ◽  
Primary Model ◽  
Shape Changes

AbstractAll blood cells originate from hematopoietic stem/progenitor cells (HSPCs). HSPCs are formed from endothelial cells (ECs) of the dorsal aorta (DA), via endothelial-to-hematopoietic transition (EHT). The zebrafish is a primary model organism to study the process in vivo. While the role of mechanical stress in controlling gene expression promoting cell differentiation is actively investigated, mechanisms driving shape changes of the DA and individual ECs remain poorly understood. We address this problem by developing a new DA micromechanical model and applying it to experimental data on zebrafish morphogenesis. The model considers the DA as an isotropic tubular membrane subjected to hydrostatic blood pressure and axial stress. The DA evolution is described as a movement in the dimensionless controlling parameters space: normalized hydrostatic pressure and axial stress. We argue that HSPC production is accompanied by two mechanical instabilities arising in the system due to the plane stress in the DA walls and show how a complex interplay between mechanical forces in the system drives the emerging morphological changes.

scholarly journals Liquid-liquid microphase separation leads to formation of membraneless organelles

2019 ◽  
Author(s):  
Srivastav Ranganathan ◽  
Eugene Shakhnovich
Keyword(s):  
Phase Separation ◽  
Rational Design ◽  
Microphase Separation ◽  
Morphological Changes ◽  
Specific Interaction ◽  
Coarse Grained ◽  
High Concentrations ◽  
Macrophase Separation

AbstractProteins and nucleic acids can spontaneously self-assemble into membraneless droplet-like compartments, both in vitro and in vivo. A key component of these droplets are multi-valent proteins that possess several adhesive domains with specific interaction partners (whose number determines total valency of the protein) separated by disordered regions. Here, using multi-scale simulations we show that such proteins self-organize into micro-phase separated droplets of various sizes as opposed to the Flory-like macro-phase separated equilibrium state of homopolymers or equilibrium physical gels. We show that the micro-phase separated state is a dynamic outcome of the interplay between two competing processes: a diffusion-limited encounter between proteins, and the dynamics within small clusters that results in exhaustion of available valencies whereby all specifically interacting domains find their interacting partners within smaller clusters, leading to arrested phase separation. We first model these multi-valent chains as bead-spring polymers with multiple adhesive domains separated by semi-flexible linkers and use Langevin Dynamics (LD) to assess how key timescales depend on the molecular properties of associating polymers. Using the time-scales from LD simulations, we develop a coarse-grained kinetic model to study this phenomenon at longer times. Consistent with LD simulations, the macro-phase separated state was only observed at high concentrations and large interaction valencies. Further, in the regime where cluster sizes approach macro-phase separation, the condensed phase becomes dynamically solid-like, suggesting that it might no longer be biologically functional. Therefore, the micro-phase separated state could be a hallmark of functional droplets formed by proteins with the sticker-spacer architecture.Significance statementMembraneless organells (MO) are ubiquitous in ‘healthy’ living cells, with an altered state in disease. Their formation is likened to liquid-liquid phase separation (LLPS) between MO-forming proteins. However most models of LLPS predict complete macrophase separation while in reality MO’s are small droplets of various sizes, which are malleable to rapid morphological changes. Here we present a microscopic multiscale theoretical study of thermodynamics and kinetics of formation of MO. We show that MO’s are long-living dynamic structures formed as a result of arrested macrophase separation. Our study provides a direct link beween the molecular properies of MO-forming proteins and the morphology and dynamics of MO paving a path to rational design and control of MO.

scholarly journals Spatially clustered loci with multiple enhancers are frequent targets of HIV-1

2018 ◽  
Author(s):  
Bojana Lucic ◽  
Heng-Chang Chen ◽  
Maja Kuzman ◽  
Eduard Zorita ◽  
Julia Wegner ◽  
...  
Keyword(s):  
T Cells ◽  
Transcriptional Activity ◽  
Nuclear Periphery ◽  
Nuclear Architecture ◽  
Gene Clusters ◽  
Nuclear Pore ◽  
Super Enhancer ◽  
First Time ◽  
Hiv 1

ABSTRACTHIV-1 recurrently targets active genes that are positioned in the outer shell of the nucleus and integrates in the proximity of the nuclear pore compartment. However, the genomic features of these genes and the relevance of their transcriptional activity for HIV-1 integration have so far remained unclear. Here we show that recurrently targeted genes are delineated with super-enhancer genomic elements and that they cluster in specific spatial compartments of the T cell nucleus. We further show that these gene clusters acquire their location at the nuclear periphery during the activation of T cells. The clustering of these genes along with their transcriptional activity are the major determinants of HIV-1 integration in T cells. Our results show for the first time the relevance of the spatial compartmentalization of the genome for HIV-1 integration, thus further strengthening the role of nuclear architecture in viral infection.

scholarly journals Role of the Nuclear Lamina in Age-Associated Nuclear Reorganization and Inflammation

Cells ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 718
Author(s):  
Lidya Kristiani ◽  
Miri Kim ◽  
Youngjo Kim
Keyword(s):  
Inflammatory Responses ◽  
Nuclear Periphery ◽  
Three Dimensional ◽  
Nuclear Lamina ◽  
Global Gene Expression ◽  
Nuclear Reorganization ◽  
Gradual Loss

Aging is characterized by the gradual loss of tissue function and integrity. Activation of inflammatory responses accelerates the deterioration of cells and tissues. Many studies have shown that alteration of the components of the nuclear lamina is associated with inflammation, both in vivo and in vitro. However, the mechanism by which the nuclear lamina regulates inflammation is largely unknown. Recent studies have suggested that the nuclear lamina regulates both organization of the three-dimensional chromatin structure at the nuclear periphery and global gene expression, such as the expression of inflammatory response genes. Here, we discuss the current updates in the research on nuclear lamina alteration, activation of inflammation, and nuclear reorganization in models of cellular senescence and organismal aging.

scholarly journals Functions and properties of nuclear lncRNAs—from systematically mapping the interactomes of lncRNAs

2020 ◽  
Vol 27 (1) ◽  
Author(s):  
Chia-Yu Guh ◽  
Yu-Hung Hsieh ◽  
Hsueh-Ping Chu
Keyword(s):  
Protein Complexes ◽  
Nuclear Organization ◽  
Regulation Of Gene Expression ◽  
Nuclear Architecture ◽  
Living Cells ◽  
Cellular Processes ◽  
Double Stranded Dna ◽  
Genome Wide ◽  
Non Coding Rnas

AbstractProtein and DNA have been considered as the major components of chromatin. But beyond that, an increasing number of studies show that RNA occupies a large amount of chromatin and acts as a regulator of nuclear architecture. A significant fraction of long non-coding RNAs (lncRNAs) prefers to stay in the nucleus and cooperate with protein complexes to modulate epigenetic regulation, phase separation, compartment formation, and nuclear organization. An RNA strand also can invade into double-stranded DNA to form RNA:DNA hybrids (R-loops) in living cells, contributing to the regulation of gene expression and genomic instability. In this review, we discuss how nuclear lncRNAs orchestrate cellular processes through their interactions with proteins and DNA and summarize the recent genome-wide techniques to study the functions of lncRNAs by revealing their interactomes in vivo.

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